Genetic Information

Gene & Transcript Details

Gene
RUNX1
Transcript
NM_001754.4 MANE Select
Total Exons
—
Reference Sequence
NC_000021.8
Alternative Transcripts
IDStatusDetails
NM_001754.3 Alternative 6190 nt | 400–1842
NM_001754.4 RefSeq Select 5967 nt | 191–1633
NM_001754.5 MANE Select 5971 nt | 195–1637

Variant Details

HGVS Notation
NM_001754.4:c.444C>T
Protein Change
T148=
Location
Exon 5 (Exon 5 of )
5
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.00566 in 100,000
Extremely Rare
ACMG Criteria Applied PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).

ClinVar

Open
Classification
Likely Benign
1 publications
Clinical Statement

"This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Likely Benign by ClinGen Myeloid Malignancy Variant Curation Expert Panel expert panel."

COSMIC Somatic Evidence

Open
COSMIC ID
COSM4101439
Recurrence
2 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
COSMIC Preview
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Functional Impact & Domains

Functional Domain

Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene RUNX1.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: RUNX1T148=RUNX1T148=SomaticNCBI Gene:861|Show additional gene information Variant OverviewRUNX1, a transcription factor involved in hematopoietic differentiation, is altered by mutation or chromosomal rearrangement in various hematologic malignancies.This is a synonymous mutation and is not annotated by OncoKB. JAX-CKB: No results found

Database Previews
OncoKB
OncoKB Preview
JAX-CKB
JAX-CKB Preview

Click on previews to view full database entries. External databases may require institutional access.

Computational Analysis

Pathogenicity Predictions

SpliceAI
Predictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied

SpliceAI Scores

Window: ±500bp
Effect Type Score Position
- Acceptor Loss (AL) 0.0 79 bp
- Donor Loss (DL) 0.01 -41 bp
+ Acceptor Gain (AG) 0.0 92 bp
+ Donor Gain (DG) 0.0 -64 bp
High impact (≥0.5) Medium impact (0.2-0.49) Low impact (<0.2)

VCEP Guidelines

Applied ACMG/AMP Criteria (VCEP Specific)

Filter Criteria:
PM2

PM2 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

BP4

BP4 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

BP6

BP6 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)