rs894763906

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001386879.1(SLCO1A2):​c.1162G>T​(p.Ala388Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000103 in 1,456,392 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A388T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.000010 ( 0 hom. )

Consequence

SLCO1A2
NM_001386879.1 missense

Scores

3
4
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.31
Variant links:
Genes affected
SLCO1A2 (HGNC:10956): (solute carrier organic anion transporter family member 1A2) This gene encodes a sodium-independent transporter which mediates cellular uptake of organic ions in the liver. Its substrates include bile acids, bromosulphophthalein, and some steroidal compounds. The protein is a member of the SLC21A family of solute carriers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2008]

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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 rank MANE Protein UniProt
SLCO1A2NM_001386879.1 linkc.1162G>T p.Ala388Ser missense_variant Exon 10 of 15 ENST00000683939.1 NP_001373808.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLCO1A2ENST00000683939.1 linkc.1162G>T p.Ala388Ser missense_variant Exon 10 of 15 NM_001386879.1 ENSP00000508235.1 P46721-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.0000103
AC:
15
AN:
1456392
Hom.:
0
Cov.:
28
AF XY:
0.00000828
AC XY:
6
AN XY:
725006
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000126
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Uncertain
0.093
D
BayesDel_noAF
Benign
-0.10
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.16
T;T
Eigen
Pathogenic
0.73
Eigen_PC
Pathogenic
0.70
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.79
T;T
M_CAP
Benign
0.038
D
MetaRNN
Uncertain
0.52
D;D
MetaSVM
Benign
-0.29
T
MutationAssessor
Uncertain
2.3
M;.
PrimateAI
Benign
0.44
T
PROVEAN
Benign
-2.1
N;N
REVEL
Benign
0.28
Sift
Benign
0.056
T;T
Sift4G
Benign
0.065
T;T
Polyphen
0.97
D;.
Vest4
0.45
MutPred
0.67
Gain of catalytic residue at W393 (P = 0);.;
MVP
0.57
MPC
0.27
ClinPred
0.99
D
GERP RS
5.2
Varity_R
0.53
gMVP
0.40

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-21448640; API