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.104G>A (p.Ser35Asn)

CA410204312

579777 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: e7ab03d1-c059-4fac-92a5-f411ddcca068

Approved on: 2024-08-12

Published on: 2024-08-12

HGVS expressions

NM_001754.5:c.104G>A

NM_001754.5(RUNX1):c.104G>A (p.Ser35Asn)

NC_000021.9:g.34887090C>T

CM000683.2:g.34887090C>T

NC_000021.8:g.36259387C>T

CM000683.1:g.36259387C>T

NC_000021.7:g.35181257C>T

NG_011402.2:g.1102622G>A

ENST00000675419.1:c.104G>A

ENST00000300305.7:c.104G>A

ENST00000344691.8:c.23G>A

ENST00000358356.9:c.23G>A

ENST00000399237.6:c.68G>A

ENST00000399240.5:c.23G>A

ENST00000437180.5:c.104G>A

ENST00000455571.5:c.65G>A

ENST00000475045.6:c.104G>A

ENST00000482318.5:c.59-6377G>A

NM_001001890.2:c.23G>A

NM_001122607.1:c.23G>A

NM_001754.4:c.104G>A

NM_001001890.3:c.23G>A

NM_001122607.2:c.23G>A

Uncertain Significance

BP4 PM2_Supporting

BA1 BP5 BP7 BP2 BP3 BP1 BS4 BS3 BS1 BS2 PP1 PP4 PP3 PP2 PS4 PS2 PS1 PS3 PM5 PM3 PM4 PM1 PVS1 PM6

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.104G>A (p.Ser35Asn) is a missense variant which has a REVEL score ≤ 0.50 (0.398) and a SpliceAI score ≤ 0.30 (0.06, 6 bp acceptor gain) (BP4). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_Supporting). In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and PM2_Supporting.

BP4

This missense variant has a REVEL score ≤0.50 (0.398) and a SpliceAI score ≤0.30 (0.06 6 bp acceptor gain) (BP4)

PM2_Supporting

This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting).

BA1

This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting).

BP5

This rule is not applicable for MM-VCEP

BP7

Not a synonymous or intronic variant

BP2

Variant absent in gnomAD

BP3

This rule is not applicable for MM-VCEP

BP1

This rule is not applicable for MM-VCEP

BS4

No case studies found

BS3

No functional studies found

BS1

This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting).

BS2

This rule is not applicable for MM-VCEP

PP1

No case studies found

PP4

This rule is not applicable for MM-VCEP

PP3

This missense variant has a REVEL score ≤0.50 (0.398) and a SpliceAI score ≤0.30 (0.06 6 bp acceptor gain) (BP4)

PP2

This rule is not applicable for MM-VCEP

PS4

No case studies found

PS2

No case studies found

PS1

Amino acid is not established as pathogenic

PS3

No functional studies found

PM5

Amino acid is not established as pathogenic

PM3

This rule is not applicable for MM-VCEP

PM4

Variant not a in-frame dleetion/insertion

PM1

Variant not in a mutational hotspot or within the critical region

PVS1

Not a null variant therefore code cannot be applied

PM6

No case studies found

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