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]
Link to SEPIO compliant JSON-LD document

Variant: NM_001754.5(RUNX1):c.138G>T (p.Ala46=)

CA10014589

1159445 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 4a44ff97-e153-42d6-8407-bc0581c11d92
Approved on: 2022-04-25
Published on: 2022-07-05

HGVS expressions

NM_001754.5:c.138G>T
NM_001754.5(RUNX1):c.138G>T (p.Ala46=)
NC_000021.9:g.34887056C>A
CM000683.2:g.34887056C>A
NC_000021.8:g.36259353C>A
CM000683.1:g.36259353C>A
NC_000021.7:g.35181223C>A
NG_011402.2:g.1102656G>T
ENST00000675419.1:c.138G>T
ENST00000300305.7:c.138G>T
ENST00000344691.8:c.57G>T
ENST00000358356.9:c.57G>T
ENST00000399237.6:c.102G>T
ENST00000399240.5:c.57G>T
ENST00000437180.5:c.138G>T
ENST00000455571.5:c.99G>T
ENST00000475045.6:c.138G>T
ENST00000482318.5:c.59-6343G>T
NM_001001890.2:c.57G>T
NM_001122607.1:c.57G>T
NM_001754.4:c.138G>T
NM_001001890.3:c.57G>T
NM_001122607.2:c.57G>T

Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 24
BA1 PP1 PP4 PP3 PP2 PM6 PM2 PM5 PM1 PM3 PM4 PVS1 BS4 BS3 BS1 BS2 BP5 BP2 BP3 BP1 PS1 PS2 PS4 PS3

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
NM_001754.5(RUNX1):c.138G>T (p.Ala46=) is a synonymous variant. REVEL score not calculable. SpliceAI predicts: Acceptor loss 0.06, Donor loss 0.02, Acceptor gain 0.00, Donor gain 0.00. (BP4) Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 1.22672 < 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 likely benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7.
Met criteria codes
BP7
Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 1.22672 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species) (BP7).
BP4
REVEL score not calculable. SpliceAI predicts: Acceptor loss 0.06, Donor loss 0.02, Acceptor gain 0.00, Donor gain 0.00. (BP4)
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No published literature could be identified for 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”
PM6
No published literature could be identified for this variant
PM2
This variant is present at very low levels (AF 0.00013, 0.013%, 1/7534 alleles with total 7534 alleles) in the African subpopulation. Therefore, PM2 is not met.
PM5
No published literature could be identified for this variant
PM1
This variant is outside the RHD.
PM3
This rule is not applicable for MM-VCEP”
PM4
Synonymous variant, not applicable
PVS1
Synonymous variant, not applicable
BS4
No published literature could be identified for this variant
BS3
No published literature could be identified for this variant
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
This rule is not applicable for MM-VCEP”
BP5
This rule is not applicable for MM-VCEP”
BP2
No published literature could be identified for this variant
BP3
This rule is not applicable for MM-VCEP”
BP1
This rule is not applicable for MM-VCEP”
PS1
No published literature could be identified for this variant
PS2
No published literature could be identified for this variant
PS4
No published literature could be identified for this variant
PS3
No published literature could be identified for this variant
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