22-50447147-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002972.4(SBF1):c.5677G>A(p.Ala1893Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,459,384 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
SBF1
NM_002972.4 missense
NM_002972.4 missense
Scores
4
9
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.56
Genes affected
SBF1 (HGNC:10542): (SET binding factor 1) This gene encodes a member of the protein-tyrosine phosphatase family. However, the encoded protein does not appear to be a catalytically active phosphatase because it lacks several amino acids in the catalytic pocket. This protein contains a Guanine nucleotide exchange factor (GEF) domain which is necessary for its role in growth and differentiation. Mutations in this gene have been associated with Charcot-Marie-Tooth disease 4B3. Pseudogenes of this gene have been defined on chromosomes 1 and 8. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBF1 | NM_002972.4 | c.5677G>A | p.Ala1893Thr | missense_variant | 41/41 | ENST00000380817.8 | |
SBF1 | NM_001410794.1 | c.5680G>A | p.Ala1894Thr | missense_variant | 41/41 | ||
SBF1 | NM_001365819.1 | c.5602G>A | p.Ala1868Thr | missense_variant | 40/40 | ||
SBF1 | NM_001410795.1 | c.5599G>A | p.Ala1867Thr | missense_variant | 40/40 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBF1 | ENST00000380817.8 | c.5677G>A | p.Ala1893Thr | missense_variant | 41/41 | 1 | NM_002972.4 | P3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243462Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133140
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GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459384Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 725968
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GnomAD4 genome Cov.: 33
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33
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Pathogenic
D;D
Vest4
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at