Variant: NM_004004.6(GJB2):c.-22-2A>C

CA6904346

375406 (ClinVar)

Gene: GJB2

Condition: nonsyndromic genetic deafness

Inheritance Mode: Autosomal recessive inheritance

UUID: 09ec9aab-7e7a-4db9-b694-2ff027effd00

HGVS expressions

NM_004004.6:c.-22-2A>C
NM_004004.6(GJB2):c.-22-2A>C
NC_000013.11:g.20189605T>G
CM000675.2:g.20189605T>G
NC_000013.10:g.20763744T>G
CM000675.1:g.20763744T>G
NC_000013.9:g.19661744T>G
NG_008358.1:g.8371A>C
ENST00000382844.2:c.-24A>C
ENST00000382848.5:c.-22-2A>C
ENST00000382844.1:c.-24A>C
ENST00000382848.4:c.-22-2A>C
NM_004004.5:c.-22-2A>C

Likely Pathogenic

• Met criteria codes: PS3_Supporting BS1 PM3_Very Strong PP1

• Not Met criteria codes: PM5 PM1 PM4 PM6 PM2 PVS1 BS2 BS4 BS3 BP3 BP2 BP1 BP4 BP5 BP7 BA1 PS1 PS2 PS4 PP4 PP2 PP3

Expert Panel

Hearing Loss VCEP

Criteria Specification Information

Evidence submitted by expert panel

Hearing Loss VCEP

The filtering allele frequency of the c.-22-2A>C variant in the GJB2 gene is 0.35% for Ashkenazi Jewish chromosomes in gnomAD v2.1.1 (95% CI of 47/10344), which meets the allele frequency threshold defined by the ClinGen Hearing Loss Expert Panel for considering strong evidence against pathogenicity for autosomal recessive hearing loss variants (BS1). However, based on the evidence outlined below, the ClinGen Hearing Loss Expert Panel believes that the evidence for the pathogenicity of this variant for nonsyndromic hearing loss outweighs its high allele frequency in population databases. Therefore, the BS1 code will not contribute to the overall classification. The c.-22-2A>C variant in the GJB2 gene has been detected in at least 9 patients with hearing loss in trans with the pathogenic c.35delG variant (PM3_Very Strong; PMID: 25401782, 24039984, 33096615; Invitae internal data, SCV000935680.2; Children’s Hospital of Philadelphia internal data, Molecular Otolaryngology and Renal Research Laboratories internal data) and one individual with the the p.Leu90Pro variant suspected in trans (PMID: 19814620). Phase was confirmed in at least 6 of these 10 observations.This variant has been reported to segregate with hearing loss in at least 2 family members (PP1; PMID: 24039984). It was also identified in the heterozygous state without a second variant in 8 individuals with hearing loss, and in the biallelic state (with c.35delG) in one individual with reportedly normal hearing (GeneDx, ARUP internal data, SCV000680741.2, SCV000603828.1). Of note, the severity of hearing loss is reported to be mild-moderate in affected probands, some with onset in the third to fourth decade, suggesting that this variant may be a hypomorphic allele. RNA analysis using patient cells demonstrated that the c.-22-2A>C variant leads to expression of a novel GJB2 transcript with a slightly longer 5' UTR but otherwise normal coding region. The alternate transcript was shown to have reduced expression, but it is not clear if the lower expression is sufficient to lead to a phenotype (PS3_Supporting; PMID: 24039984). In summary, the VCEP has used expert judgement to classify this variant as likely pathogenic for autosomal recessive hearing loss based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM3_Very Strong, PP1, PS3_Supporting, BS1.

Met criteria codes

• PS3_Supporting: Gandia 2013 performed RT-PCR on patient cells with the c.-22-2A>C/c.35delG genotype. They showed that the wild-type splice acceptor site is completely abolished by the -22-2A>C variant, and two alternative splice sites are used that are 34 and 38 nucleotides upstream of the known splice site. No normal transcript was detected in patient cells.
• BS1: In gnomAD v2, present in 0.4544% (47/10344) of Ashkenazi Jewish chromosomes (lower bound of the 95% CI is 0.35%) and 0.07895% (100/126668) of non-Finnish European chromosomes. In v3, present in 0.49813% (16/3324) of Ashkenazi Jewish chromosomes; next highest frequency is 0.1025% (14/13662) of Latino chromosomes.
• PM3_Very Strong: The c.-22-2A>C variant has been observed in trans with c.35delG in 9 individuals (Gandia et al PMID: 24039984, Stanghellini et al PMID: 25401782, Buonfiglio et al PMID: 33096615, MORL internal data, Invitae SCV000935680.2, CHOP internal data). Most individuals had mild-moderate hearing loss. It has also been observed in trans with the p.Leu90Pro variant (Sansovic et al PMID: 25401782). Total: 10 cases, 6 were confirmed in trans, 4 were suspected in trans. Total PM3 points count is 8 points, which corresponds to PM3_Very Strong
• PP1: The c.-22-2A>C variant was identified in three family members in compound heterozygosity with c.35delG. Two affected segregations are counted here.

Not Met criteria codes

• PM5: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM6: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PVS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BS2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BS4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BS3: Gandia 2013 performed RT-PCR on patient cells with the c.-22-2A>C/c.35delG genotype. They showed that the wild-type splice acceptor site is completely abolished by the -22-2A>C variant, and two alternative splice sites are used that are 34 and 38 nucleotides upstream of the known splice site. No normal transcript was detected in patient cells.
• BP3: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BP2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BP1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BP4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BP5: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BP7: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BA1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PP4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PP2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PP3: Splice predictor tools all predict wt 3' splice acceptor is abolished by this variant. Some (GeneSplicer and Human Splicing Finder) predict that a novel splice acceptor site is formed 2 bases downstream. However, to avoid double-counting splice effect accounted for by experimental evidence, PP3 was not applied. PS2_Supporting was applied instead.

Approved on: 2021-04-12

Published on: 2024-01-11