rs976154000
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030622.8(CYP2S1):c.23C>A(p.Ala8Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CYP2S1
NM_030622.8 missense
NM_030622.8 missense
Scores
4
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.16
Genes affected
CYP2S1 (HGNC:15654): (cytochrome P450 family 2 subfamily S member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum. In rodents, the homologous protein has been shown to metabolize certain carcinogens; however, the specific function of the human protein has not been determined. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18125415).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CYP2S1 | NM_030622.8 | c.23C>A | p.Ala8Glu | missense_variant | Exon 1 of 9 | ENST00000310054.9 | NP_085125.1 | |
| CYP2S1 | XM_047438711.1 | c.23C>A | p.Ala8Glu | missense_variant | Exon 1 of 7 | XP_047294667.1 | ||
| LOC124904790 | XM_047439802.1 | c.-235G>T | upstream_gene_variant | XP_047295758.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CYP2S1 | ENST00000310054.9 | c.23C>A | p.Ala8Glu | missense_variant | Exon 1 of 9 | 1 | NM_030622.8 | ENSP00000308032.3 | ||
| CYP2S1 | ENST00000600561.1 | c.23C>A | p.Ala8Glu | missense_variant | Exon 1 of 4 | 2 | ENSP00000471016.1 | |||
| CYP2S1 | ENST00000597754.1 | c.23C>A | p.Ala8Glu | missense_variant | Exon 1 of 4 | 5 | ENSP00000471637.1 | |||
| CYP2S1 | ENST00000593545.5 | n.23C>A | non_coding_transcript_exon_variant | Exon 1 of 6 | 2 | ENSP00000472555.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1389158Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 685500
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1389158
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
685500
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.
REVEL
Uncertain
Sift
Benign
T;.;.
Sift4G
Benign
T;T;T
Polyphen
B;.;.
Vest4
MutPred
Loss of helix (P = 0.0167);Loss of helix (P = 0.0167);Loss of helix (P = 0.0167);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at