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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Variant: NM_001754.4(RUNX1):c.729A>C (p.Pro243=)

CA320603666

436613 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 9f45b964-b1a9-4ec5-b6e4-e9be27b7aa84
Approved on: 2021-06-25
Published on: 2023-11-13

HGVS expressions

NM_001754.4:c.729A>C
NM_001754.4(RUNX1):c.729A>C (p.Pro243=)
NC_000021.9:g.34834486T>G
CM000683.2:g.34834486T>G
NC_000021.8:g.36206783T>G
CM000683.1:g.36206783T>G
NC_000021.7:g.35128653T>G
NG_011402.2:g.1155226A>C
ENST00000675419.1:c.729A>C
ENST00000300305.7:c.729A>C
ENST00000344691.8:c.648A>C
ENST00000358356.9:c.648A>C
ENST00000399237.6:c.693A>C
ENST00000399240.5:c.532+24988A>C
ENST00000437180.5:c.729A>C
ENST00000469087.1:n.265A>C
ENST00000482318.5:c.*319A>C
NM_001001890.2:c.648A>C
NM_001122607.1:c.648A>C
NM_001001890.3:c.648A>C
NM_001122607.2:c.648A>C
NM_001754.5:c.729A>C
NM_001754.5(RUNX1):c.729A>C (p.Pro243=)
More

Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 23
PP1 PP4 PP3 PP2 PM6 PM2 PM3 PM1 PM4 PM5 BS2 BS3 BS1 BP5 BP2 BP3 BP1 PVS1 PS3 PS2 PS4 PS1 BA1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
This synonymous variant is predicted by SSF, MES, and SpliceAI to lead to either no change/an increase/a decrease by no more than 10% in the canonical splice site score and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score = 0.975787 in GRCh37/1.06724 in GRCh38 or the variant is the reference nucleotide in one primate and/or three mammal species) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7.
Met criteria codes
BP7
This synonymous variant is predicted by SSF, MES, and SpliceAI to lead to either no change/an increase/a decrease by no more than 10% in the canonical splice site score and no putative cryptic splice sites are created. However, evolutionary conservation prediction algorithms predict the site as being weakly conserved (PhyloP score = 0.975787 in GRCh37/1.06724 in GRCh38), and the variant is not the reference nucleotide in one primate and/or three mammal species (only in the lesser Egyptian jerboa and hedgehog).
BP4
This synonymous variant is predicted by SSF, MES, and SpliceAI to lead to either no change/an increase/a decrease by no more than 10% in the canonical splice site score, and no putative cryptic splice sites are created.
Not Met criteria codes
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Not applicable
PP3
This synonymous variant is predicted by SSF, MES, and SpliceAI to lead to either no change/an increase/a decrease by no more than 10% in the canonical splice site score, and no putative cryptic splice sites are created.
PP2
Not applicable
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
gnomAD v2: Absent (>20x coverage) gnomAD v3: ALL:0.001410% (2/141824 alleles) - AFR:0.004832% (2/41392 alleles, no homozygotes)
PM3
Not applicable
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
Not applicable
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
gnomAD v2: Absent (>20x coverage) gnomAD v3: ALL:0.001410% (2/141824 alleles) - AFR:0.004832% (2/41392 alleles, no homozygotes)
BP5
Not applicable
BP2
No homozygotes reported in gnomAD. No case reports.
BP3
Not applicable
BP1
Not applicable
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
gnomAD v2: Absent (>20x coverage) gnomAD v3: ALL:0.001410% (2/141824 alleles) - AFR:0.004832% (2/41392 alleles, no homozygotes)
Curation History
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