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]
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  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_001754.5(RUNX1):c.98-4G>A

CA320642989

1077574 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: f8e59f84-0b1d-451a-b6ac-52b3af8c8dca
Approved on: 2024-07-17
Published on: 2024-07-17

HGVS expressions

NM_001754.5:c.98-4G>A
NM_001754.5(RUNX1):c.98-4G>A
NC_000021.9:g.34887100C>T
CM000683.2:g.34887100C>T
NC_000021.8:g.36259397C>T
CM000683.1:g.36259397C>T
NC_000021.7:g.35181267C>T
NG_011402.2:g.1102612G>A
ENST00000675419.1:c.98-4G>A
ENST00000300305.7:c.98-4G>A
ENST00000344691.8:c.13G>A
ENST00000358356.9:c.13G>A
ENST00000399237.6:c.62-4G>A
ENST00000399240.5:c.13G>A
ENST00000437180.5:c.98-4G>A
ENST00000455571.5:c.59-4G>A
ENST00000475045.6:c.98-4G>A
ENST00000482318.5:c.59-6387G>A
NM_001001890.2:c.13G>A
NM_001122607.1:c.13G>A
NM_001754.4:c.98-4G>A
NM_001001890.3:c.13G>A
NM_001122607.2:c.13G>A

Uncertain Significance

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

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
The NM_001754.5(RUNX1):c.98-4G>A is an intronic variant which is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting). It has not been reported in any individuals meeting at least one of the RUNX1-phenotypic criteria. This intronic variant has a SpliceAI score ≤ 0.20 (0.0) (BP4). In summary, this variant meets criteria to be classified as a variant of uncertain significance. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM2_supporting, BP4.
Met criteria codes
BP4
REVEL score= 0.465 (BP4 ≤ 0.50), no splice effect predicted
PM2_Supporting
This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (gnomAD v2.1.1 and v3)
Not Met criteria codes
BS2
This rule is not applicable for MM-VCEP
BS4
No case study found
BS3
No functional studies found
BS1
PM2 met
PVS1
This is not a null variant
PS4
No case studies found
PS2
No case study found
PS1
Not a missense variant
PS3
No functional studies found
BP2
No case study found
BP3
This rule is not applicable for MM-VCEP
BP1
This rule is not applicable for MM-VCEP
BP7
No splice effect is predicted (SpliceAI) however the nucleotide is conserved (PhyloP =3.60587)
BP5
This rule is not applicable for MM-VCEP
BA1
PM2 met
PP1
No case studies found
PP4
This rule is not applicable for MM-VCEP
PP3
BP4 met
PP2
This rule is not applicable for MM-VCEP
PM5
Not a missense variant
PM1
Intronic variant not located in hot-spot or functional domain
PM3
This rule is not applicable for MM-VCEP
PM4
Intronic variant
PM6
No case study found
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