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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0770
Variant links:
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]

Genome browser will be placed here

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
SPTSSBNM_001040100.2 linkuse as main transcriptc.-125-4299A>T intron_variant ENST00000620149.2 NP_001035189.1
SPTSSBNM_001320679.2 linkuse as main transcriptc.-264-4299A>T intron_variant NP_001307608.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPTSSBENST00000620149.2 linkuse as main transcriptc.-125-4299A>T intron_variant NM_001040100.2 ENSP00000480827 P1
SPTSSBENST00000359175.9 linkuse as main transcriptc.-125-4299A>T intron_variant 1 ENSP00000352097 P1
SPTSSBENST00000497137.1 linkuse as main transcriptc.-264-4299A>T intron_variant 3 ENSP00000420115 P1
SPTSSBENST00000497374.1 linkuse as main transcriptn.84-4299A>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.647
AC:
98115
AN:
151702
Hom.:
33812
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.853
Gnomad AMI
AF:
0.470
Gnomad AMR
AF:
0.696
Gnomad ASJ
AF:
0.596
Gnomad EAS
AF:
0.966
Gnomad SAS
AF:
0.743
Gnomad FIN
AF:
0.498
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.508
Gnomad OTH
AF:
0.614
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.647
AC:
98235
AN:
151820
Hom.:
33873
Cov.:
30
AF XY:
0.651
AC XY:
48271
AN XY:
74194
show subpopulations
Gnomad4 AFR
AF:
0.853
Gnomad4 AMR
AF:
0.696
Gnomad4 ASJ
AF:
0.596
Gnomad4 EAS
AF:
0.966
Gnomad4 SAS
AF:
0.742
Gnomad4 FIN
AF:
0.498
Gnomad4 NFE
AF:
0.508
Gnomad4 OTH
AF:
0.619
Alfa
AF:
0.446
Hom.:
1236
Bravo
AF:
0.670
Asia WGS
AF:
0.855
AC:
2971
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.1
DANN
Benign
0.29

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs336583; hg19: chr3-161081981; API