Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: SOS2 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_006939.4(SOS2):c.2600A>G (p.Asn867Ser)

CA7177004

506639 (ClinVar)

Gene: SOS2
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 50571ee3-87fa-4046-b73a-9af9e3b1cb03
Approved on: 2024-12-03
Published on: 2025-03-25

HGVS expressions

NM_006939.4:c.2600A>G
NM_006939.4(SOS2):c.2600A>G (p.Asn867Ser)
NC_000014.9:g.50145237T>C
CM000676.2:g.50145237T>C
NC_000014.8:g.50611955T>C
CM000676.1:g.50611955T>C
NC_000014.7:g.49681705T>C
NG_051073.1:g.91457A>G
ENST00000216373.10:c.2600A>G
ENST00000216373.9:c.2600A>G
ENST00000543680.5:c.2501A>G
NM_006939.2:c.2600A>G
NM_006939.3:c.2600A>G
More

Likely Benign

Met criteria codes 2
BP4 BS1
Not Met criteria codes 2
BA1 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SOS2 Version 2.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.2600A>G (NM_006939.4(SOS2):c.2600A>G (p.Asn867Ser)) variant in SOS2 is a missense variant predicted to cause substitution of asparagine by serine at amino acid 867. The filtering allele frequency in gnomAD v2.1.1 is 0.03346 % (BS1). The computational predictor REVEL gives a score of 0.182 which is below the threshold of 0.3, evidence that does not predict a damaging effect on SOS2 function (BP4). In summary, this variant meets the criteria to be classified as likely benign for autosomal dominant RASopathy, based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: BS1, BP4 (Version 2.3; 12/3/2024).
Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.182 which is below the threshold of 0.3, evidence that does not predict a damaging effect on SOS2 function (BP4).
BS1
The filtering allele frequency in gnomAD v2.1.1 is 0.03346 % (BS1).
Not Met criteria codes
BA1
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
Curation History
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