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]

Variant: NM_001754.5(RUNX1):c.1086G>T (p.Ser362=)

CA10014208

1078219 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 7f409c13-8f7f-4bd1-a46f-2a06bc3ceced
Approved on: 2022-07-05
Published on: 2022-07-05

HGVS expressions

NM_001754.5:c.1086G>T
NM_001754.5(RUNX1):c.1086G>T (p.Ser362=)
NC_000021.9:g.34792492C>A
CM000683.2:g.34792492C>A
NC_000021.8:g.36164789C>A
CM000683.1:g.36164789C>A
NC_000021.7:g.35086659C>A
NG_011402.2:g.1197220G>T
ENST00000675419.1:c.1086G>T
ENST00000300305.7:c.1086G>T
ENST00000344691.8:c.1005G>T
ENST00000399240.5:c.813G>T
ENST00000437180.5:c.1086G>T
ENST00000482318.5:c.*676G>T
NM_001001890.2:c.1005G>T
NM_001754.4:c.1086G>T
NM_001001890.3:c.1005G>T
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Benign

The Expert Panel has overridden the computationally generated classification - "Likely Benign"
Met criteria codes 3
BS1 BP4 BP7
Not Met criteria codes 23
BS2 BS4 BS3 BP2 BP3 BP1 BP5 PS2 PS4 PS3 PS1 BA1 PP1 PP4 PP3 PP2 PM1 PM5 PM3 PM4 PM6 PM2 PVS1

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.1086G>T (p.Ser362=) is a synonymous variant. AF 0.0006271 (0.06271%)( 10/15946 in East Asian subpopulation in gnomAD v2.1.1.) is 0.015% between 0.15% (BS1). REVEL score not calculable as this is a synonymous variant. SpliceAI predicts the following: Acceptor loss 0.00, Donor loss 0.00, Acceptor gain 0.00, Donor gain 0.00 (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.503315 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species) (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: BS1, BP4, BP7.
Met criteria codes
BS1
MAF 0.0006271 (0.06271%)( 10/15946 in East Asian subpopulation in gnomAD v2.1.1.) is 0.015% between 0.15%
BP4
REVEL score not calculable as this is a synonymous variant. SpliceAI predicts the following: Acceptor loss 0.00, Donor loss 0.00, Acceptor gain 0.00, Donor gain 0.00.
BP7
Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.503315 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species) (BP7).
Not Met criteria codes
BS2
This rule is not applicable for MM-VCEP
BS4
No published literature is available on this variant
BS3
No published literature is available on this variant
BP2
No published literature is available on this variant
BP3
This rule is not applicable for MM-VCEP
BP1
This rule is not applicable for MM-VCEP
BP5
This rule is not applicable for MM-VCEP
PS2
No published literature is available on this variant
PS4
No published literature is available on this variant
PS3
No published literature is available on this variant
PS1
Synonymous variant, not applicable.
BA1
MAF 0.0006271 (0.06271%)( 10/15946 in East Asian subpopulation in gnomAD v2.1.1.) is 0.015% between 0.15%
PP1
No published literature is available on this variant
PP4
This rule is not applicable for MM-VCEP
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
This rule is not applicable for MM-VCEP
PM1
This variant occurs outside of the established Runt homology domain (RHD)
PM5
Synonymous variant, not applicable.
PM3
This rule is not applicable for MM-VCEP
PM4
Synonymous variant
PM6
No published literature is available on this variant
PM2
MAF 0.0006271 (0.06271%)( 10/15946 in East Asian subpopulation in gnomAD v2.1.1.) is 0.015% between 0.15%
PVS1
Synonymous variant, not applicable.
Curation History
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