rs336583
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040100.2(SPTSSB):c.-125-4299A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,820 control chromosomes in the GnomAD database, including 33,873 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.65 ( 33873 hom., cov: 30)
Consequence
SPTSSB
NM_001040100.2 intron
NM_001040100.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0770
Genes affected
SPTSSB (HGNC:24045): (serine palmitoyltransferase small subunit B) Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTB is a small SPT subunit that stimulates SPT activity and confers acyl-CoA preference to the SPT catalytic heterodimer of SPTLC1 (MIM 605712) and either SPTLC2 (MIM 605713) or SPTLC3 (MIM 611120) (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPTSSB | NM_001040100.2 | c.-125-4299A>T | intron_variant | ENST00000620149.2 | NP_001035189.1 | |||
SPTSSB | NM_001320679.2 | c.-264-4299A>T | intron_variant | NP_001307608.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPTSSB | ENST00000620149.2 | c.-125-4299A>T | intron_variant | NM_001040100.2 | ENSP00000480827 | P1 | ||||
SPTSSB | ENST00000359175.9 | c.-125-4299A>T | intron_variant | 1 | ENSP00000352097 | P1 | ||||
SPTSSB | ENST00000497137.1 | c.-264-4299A>T | intron_variant | 3 | ENSP00000420115 | P1 | ||||
SPTSSB | ENST00000497374.1 | n.84-4299A>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.647 AC: 98115AN: 151702Hom.: 33812 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.647 AC: 98235AN: 151820Hom.: 33873 Cov.: 30 AF XY: 0.651 AC XY: 48271AN XY: 74194
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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