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 computed assertion could be determined for this classification!


Variant: NM_001754.5(RUNX1):c.102C>A (p.Ala34=)

CA512319000

2834488 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 73c19fa8-91f2-4534-bc1c-91274809e819
Approved on: 2024-10-29
Published on: 2024-10-29

HGVS expressions

NM_001754.5:c.102C>A
NM_001754.5(RUNX1):c.102C>A (p.Ala34=)
NC_000021.9:g.34887092G>T
CM000683.2:g.34887092G>T
NC_000021.8:g.36259389G>T
CM000683.1:g.36259389G>T
NC_000021.7:g.35181259G>T
NG_011402.2:g.1102620C>A
ENST00000675419.1:c.102C>A
ENST00000300305.7:c.102C>A
ENST00000344691.8:c.21C>A
ENST00000358356.9:c.21C>A
ENST00000399237.6:c.66C>A
ENST00000399240.5:c.21C>A
ENST00000437180.5:c.102C>A
ENST00000455571.5:c.63C>A
ENST00000475045.6:c.102C>A
ENST00000482318.5:c.59-6379C>A
NM_001001890.2:c.21C>A
NM_001122607.1:c.21C>A
NM_001754.4:c.102C>A
NM_001001890.3:c.21C>A
NM_001122607.2:c.21C>A
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Uncertain Significance

Met criteria codes 2
PM2_Supporting BP4
Not Met criteria codes 24
PM6 PS2 PS4 PS3 PS1 BA1 PM1 PM5 PM3 PM4 PP1 PP4 PP3 PP2 PVS1 BS2 BS4 BS3 BS1 BP7 BP5 BP2 BP3 BP1

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.102C>A (p.Ala34=) is a synonymous variant which has a SpliceAI score ≤ 0.20 (0.03) (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, PM2_supporting.
Met criteria codes
PM2_Supporting
This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_Supporting).
BP4
This synonymous variant has a SpliceAI score ≤ 0.20 (0.03) (BP4).
Not Met criteria codes
PM6
De novo data for this variant has not been reported in literature.
PS2
De novo data for this variant has not been reported in literature.
PS4
Proband data for this variant has not been reported in literature.
PS3
In vitro or in vivo functional data has not been reported for this variant in the literature.
PS1
This variant is not a missense variant.
BA1
This variant does not have a MAF ≥ 0.0015 (0.15%) in any general continental population dataset.
PM1
This variant is not a missense variant.
PM5
This variant is not a missense variant.
PM3
This rule is not applicable for MM-VCEP.
PM4
This variant is not an in-frame deletion/insertion.
PP1
Segregation data for this variant has not been reported in literature.
PP4
This rule is not applicable for MM-VCEP.
PP3
This synonymous or intronic variant does not have a REVEL score ≥ 0.88 or a SpliceAI score ≥ 0.38.
PP2
This rule is not applicable for MM-VCEP.
PVS1
This variant is not a null variant.
BS2
This rule is not applicable for MM-VCEP.
BS4
Segregation data for this variant has not been reported in literature.
BS3
In vitro or in vivo functional data has not been reported for this variant in the literature.
BS1
This variant does not have a MAF between 0.00015 (0.015%) and 0.0015 (0.15%) in any general continental dataset.
BP7
This variant does not have a phyloP score < 2.0.
BP5
This rule is not applicable for MM-VCEP.
BP2
This variant has not been observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
BP3
This rule is not applicable for MM-VCEP.
BP1
This rule is not applicable for MM-VCEP.
Curation History
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