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 obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_001754.5(RUNX1):c.*2532G>A

CA10652913

339828 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 0ed18044-9686-47f2-949b-66781b02a535
Approved on: 2024-09-10
Published on: 2024-09-10

HGVS expressions

NM_001754.5:c.*2532G>A
NM_001754.5(RUNX1):c.*2532G>A
NC_000021.9:g.34789603C>T
CM000683.2:g.34789603C>T
NC_000021.8:g.36161900C>T
CM000683.1:g.36161900C>T
NC_000021.7:g.35083770C>T
NG_011402.2:g.1200109G>A
ENST00000675419.1:c.*2532G>A
ENST00000300305.7:c.*2532G>A
ENST00000344691.8:c.*2532G>A
ENST00000437180.5:c.*2532G>A
NM_001001890.2:c.*2532G>A
NM_001754.4:c.*2532G>A
NM_001001890.3:c.*2532G>A
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Benign

Met criteria codes 3
BP7 BP4 BA1
Not Met criteria codes 23
BS2 BS4 BS3 BS1 BP5 BP2 BP3 BP1 PS2 PS4 PS3 PS1 PP1 PP4 PP3 PP2 PVS1 PM6 PM2 PM1 PM5 PM3 PM4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Myeloid Malignancy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
NM_001754.5(RUNX1):c.*2532G>A is a variant within the 3'UTR. Its minor allele frequency (MAF) of 0.003724 (0.3724%, 32/8594 alleles) in the Ashkenazi Jewish subpopulation of the gnomAD v4.0.0 cohort is ≥ 0.0015 (0.15%) (BA1). This variant has a SpliceAI score ≤ 0.20 (0.0) and does not have an impact on the protein (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score ≤ 2.0 (-1.16)) (BP7). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP4, BP7.
Met criteria codes
BP7
This variant has a SpliceAI score ≤ 0.20 (0.0) and evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score ≤ 2.0 (-1.16)) (BP7).
BP4
This variant has a SpliceAI score ≤ 0.20 (0.0) and does not have an impact on the protein (BP4).
BA1
MAF of 0.003724 (0.3724%, 32/8594, 32 alleles) in the Ashkenazi Jewish subpopulation of the gnomAD v4.0.0 cohort is ≥ 0.0015 (0.15%) (BA1).
Not Met criteria codes
BS2
This rule is not applicable for MM-VCEP.
BS4
This variant has no data demonstrating segregation in affected family members.
BS3
This variant has no functional studies demonstrating damaging effect on protein function or splicing.
BS1
This variant does not have a MAF between 0.00015 (0.015%) and 0.0015 (0.15%) in any general continental dataset.
BP5
This rule is not applicable for MM-VCEP.
BP2
This nonsense variant does not have any observed cases reported in the literature.
BP3
This rule is not applicable for MM-VCEP.
BP1
This rule is not applicable for MM-VCEP.
PS2
This nonsense variant does not have data on cases in patients with the disease and no family history.
PS4
This rule is not applicable because there is no published information on affected individuals nor a RUNX1 case control study. This variant was reported in ClinVar in 2018 (updated in 2020) by Illumina Laboratory Services, Illumina but the affected status of the proband is unknown (Variation ID 339828).
PS3
This variant has no functional studies demonstrating damaging effect on the gene or gene product.
PS1
This missense variant is in a non-coding region of RUNX1.
PP1
This variant has no data demonstrating cosegregation with disease in multiple affected family members in RUNX1.
PP4
This rule is not applicable for MM-VCEP.
PP3
This is a nonsense variant in the 3'UTR of RUNX1.
PP2
This rule is not applicable for MM-VCEP.
PVS1
This variant is not a null variant.
PM6
This nonsense variant does not have data on probands meeting at least one of the RUNX1-phenotypic criteria with assumed de novo occurrences.
PM2
This variant is present in at least one population database.
PM1
This nonsense variant does not affect one of the hotspot residues established by the MM-VCEP for RUNX1.
PM5
This missense variant is in a non-coding region of RUNX1.
PM3
This rule is not applicable for MM-VCEP.
PM4
This is a nonsense variant in the 3'UTR.
Curation History
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