Genetic Information
Gene & Transcript Details
Gene
SF3B1
Transcript
NM_012433.2
MANE Select
Total Exons
—
Reference Sequence
NC_000002.11
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_012433.2 | Alternative | 4314 nt | 49–3963 |
| NM_012433.3 | RefSeq Select | 4338 nt | 95–4009 |
| NM_012433.4 | MANE Select | 6463 nt | 30–3944 |
Variant Details
HGVS Notation
NM_012433.2:c.1876A>G
Protein Change
N626D
Location
Exon 14
(Exon 14 of )
14
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—
Clinical & Population Data
Population Frequency
gnomAD Global Frequency
0.000398 in 100,000
Extremely Rare
ACMG Criteria Applied
PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).
ClinVar
OpenClassification
Unknown
0 publications
Clinical Statement
""
COSMIC Somatic Evidence
OpenCOSMIC ID
COSM131555
Recurrence
12 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
Accessing full COSMIC database details requires institutional login or subscription.
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 SF3B1.
Functional Summary
Error in OpenAI Consolidation. OncoKB: SF3B1N626DSF3B1N626DSomaticNCBI Gene:23451|Show additional gene information Variant OverviewSF3B1, a component of the spliceosome complex, is frequently mutated in hematologic malignancies.There is no available functional data about the SF3B1 N626D mutation (last reviewed on 02/02/2023). However, it has been identified as a statistically significant hotspot and is likely to be oncogenic. JAX-CKB: No results found
Database Previews
OncoKB
JAX-CKB
Click on previews to view full database entries. External databases may require institutional access.
Computational Analysis
Pathogenicity Predictions
SpliceAIPredictor Consensus
Pathogenic
PP3 Applied
Yes
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied
SpliceAI Scores
Window: ±500bp| Effect Type | Score | Position |
|---|---|---|
| Acceptor Loss (AL) | 0.02 | -244 bp |
| Donor Loss (DL) | 0.08 | 11 bp |
| Acceptor Gain (AG) | 0.0 | 69 bp |
| Donor Gain (DG) | 0.04 | -114 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:
PS3
PS3 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
PM2
PM2 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
PP3
PP3 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)