Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

Variant: NM_001754.5(RUNX1):c.367G>A (p.Asp123Asn)

CA10014525

861043 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 2952c0e5-2865-49c9-ae6d-9531aea72559

Approved on: 2022-07-05

Published on: 2022-07-05

HGVS expressions

NM_001754.5:c.367G>A

NM_001754.5(RUNX1):c.367G>A (p.Asp123Asn)

NC_000021.9:g.34880698C>T

CM000683.2:g.34880698C>T

NC_000021.8:g.36252995C>T

CM000683.1:g.36252995C>T

NC_000021.7:g.35174865C>T

NG_011402.2:g.1109014G>A

ENST00000675419.1:c.367G>A

ENST00000300305.7:c.367G>A

ENST00000344691.8:c.286G>A

ENST00000358356.9:c.286G>A

ENST00000399237.6:c.331G>A

ENST00000399240.5:c.286G>A

ENST00000437180.5:c.367G>A

ENST00000455571.5:c.328G>A

ENST00000482318.5:c.74G>A

NM_001001890.2:c.286G>A

NM_001122607.1:c.286G>A

NM_001754.4:c.367G>A

NM_001001890.3:c.286G>A

NM_001122607.2:c.286G>A

Uncertain Significance

PM1_Supporting

BS4 BS3 BS1 BS2 BP7 BP5 BP2 BP3 BP4 BP1 PS4 PS2 PS1 PS3 PP1 PP4 PP3 PP2 PM6 PM2 PVS1 PM5 PM3 PM4 BA1

Evidence Links 0

Expert Panel

Myeloid Malignancy VCEP

Criteria Specification Information

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

PDF

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

NM_001754.5(RUNX1):c.367G>A (p.Asp123Asn) is a missense variant. This variant is present 2 times in gnomAD v3.1.2. MAF of 0.00002940 (0.002940%, 2/ 68022 in the European non-Finnish subpopulation. This variant affects one of the other residues (AA 89-204) within the RHD (PM1_Supporting). In summary, this variant meets criteria to be classified as variant of uncertain significance. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM1_supporting.

PM1_Supporting

This variant affects one of the other residues (AA 89-204) within the RHD (PM1_SUPPORTING CLASSIFICATION).

BS4

No case study found

BS3

No studies found

BS1

MAF of 0.00002940 (0.002940%, 2/ 68022 in the European non-Finnish subpopulation of gnomAD v3.1.2.

BS2

This rule is not applicable for MM-VCEP

BP7

This is a missense variant

BP5

This rule is not applicable for MM-VCEP

BP2

No case study found

BP3

This rule is not applicable for MM-VCEP

BP4

This missense variant has a REVEL score >0.5

BP1

This rule is not applicable for MM-VCEP

PS4

1 proband has been observed in ClinVar without any phenotypic data provided

PS2

No case study found

PS1

This is not the same amino acid change as a previously seen pathogenic variant

PS3

No studies found

PP1

No case study found

PP4

This rule is not applicable for MM-VCEP

PP3

This missense variant has a REVEL score<0.88 (0.803)

PP2

This rule is not applicable for MM-VCEP

PM6

No case study found

PM2

MAF of 0.00002940 (0.002940%, 2/ 68022 in the European non-Finnish subpopulation of gnomAD v3.1.2.

PVS1

This is a missense variant

PM5

This is not a novel missense change at an amino acid residue where a pathogenic variant has been seen before

PM3

This rule is not applicable for MM-VCEP

PM4

This is a Missense variant

BA1

MAF of 0.00002940 (0.002940%, 2/ 68022 in the European non-Finnish subpopulation of gnomAD v3.1.2.

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