11-75193317-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_007256.5(SLCO2B1):c.1175C>T(p.Thr392Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,804 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SLCO2B1
NM_007256.5 missense
NM_007256.5 missense
Scores
2
1
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.55
Publications
33 publications found
Genes affected
SLCO2B1 (HGNC:10962): (solute carrier organic anion transporter family member 2B1) This locus encodes a member of the organic anion-transporting polypeptide family of membrane proteins. The protein encoded by this locus may function in regulation of placental uptake of sulfated steroids. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 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 |
|---|---|---|---|---|---|---|---|---|
| SLCO2B1 | NM_007256.5 | c.1175C>T | p.Thr392Ile | missense_variant | Exon 9 of 14 | ENST00000289575.10 | NP_009187.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLCO2B1 | ENST00000289575.10 | c.1175C>T | p.Thr392Ile | missense_variant | Exon 9 of 14 | 1 | NM_007256.5 | ENSP00000289575.5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461804Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727192 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1461804
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
727192
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
1
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
53340
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1112004
Other (OTH)
AF:
AC:
1
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_noAF
Benign
DEOGEN2
Benign
.;T;.;.;.
LIST_S2
Benign
T;T;T;.;.
MetaRNN
Uncertain
D;D;D;D;D
MutationAssessor
Benign
.;.;.;.;.
PhyloP100
PROVEAN
Benign
.;.;.;.;.
REVEL
Benign
Sift
Pathogenic
.;.;.;.;.
Sift4G
Pathogenic
D;T;T;D;D
Vest4
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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