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]
  • See Evidence submitted by expert panel for details.

Variant: NM_001754.4(RUNX1):c.1086G>C (p.Ser362=)

CA10014207

415828 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ce8d15b3-b9f0-4e41-bd0d-9e4806b3eaae
Approved on: 2020-01-13
Published on: 2020-01-14

HGVS expressions

NM_001754.4:c.1086G>C
NM_001754.4(RUNX1):c.1086G>C (p.Ser362=)
NC_000021.9:g.34792492C>G
CM000683.2:g.34792492C>G
NC_000021.8:g.36164789C>G
CM000683.1:g.36164789C>G
NC_000021.7:g.35086659C>G
NG_011402.2:g.1197220G>C
NM_001001890.2:c.1005G>C
ENST00000300305.7:c.1086G>C
ENST00000344691.8:c.1005G>C
ENST00000399240.5:c.813G>C
ENST00000437180.5:c.1086G>C
ENST00000482318.5:c.*676G>C
More

Benign

Met criteria codes 3
BA1 BP7 BP4
Not Met criteria codes 15
PVS1 PS3 PS4 PS1 PP3 PP1 PM2 PM6 PM1 PM4 PM5 BS1 BS3 BS4 BP2

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
This synonymous variant has a MAF of 0.002828 (0.2828%, 61/21570, 43140 alleles) in the African (gnomAD) cohort is ≥ 0.0015 (0.15%) (BA1). It is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -0.12 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP4, and BP7.
Met criteria codes
BA1
MAF of 0.002828 (0.2828%, 61/21570, 43140 alleles) in the African (gnomAD) cohort is ≥ 0.0015 (0.15%)
BP7
This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created. In addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -0.12 < 0.1 [-14.1;6.4]).
BP4
This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created.
Not Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
PS4 cannot be applied because the variant presents more than 2 times in gnomAD.
4 SNPs (including S362S) were detected in 10/470 adult patients with de novo non-M3 AML, but were excluded from analysis. PubMed:19808697
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
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
PM6
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
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
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
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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