Variant rs35199625 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007256.5(SLCO2B1):c.601G>A(p.Val201Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,614,034 control chromosomes in the GnomAD database, including 301 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.013 ( 27 hom., cov: 32)

Exomes 𝑓: 0.015 ( 274 hom. )

Consequence

SLCO2B1
NM_007256.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.42

Variant links:

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]

SLCO2B1 links:

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 (MetaRNN=0.008726269).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO2B1	NM_007256.5 linkuse as main transcript	c.601G>A	p.Val201Met	missense_variant	5/14	ENST00000289575.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO2B1	ENST00000289575.10 linkuse as main transcript	c.601G>A	p.Val201Met	missense_variant	5/14	1	NM_007256.5	P2

Frequencies

GnomAD3 genomes

AF:

0.0129

AC:

1958

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00292

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0163

Gnomad ASJ

AF:

0.0184

Gnomad EAS

AF:

0.0627

Gnomad SAS

AF:

0.0392

Gnomad FIN

AF:

0.0207

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.0208

AC:

5224

AN:

251208

Hom.:

AF XY:

0.0209

AC XY:

2834

AN XY:

135772

show subpopulations

Gnomad AFR exome

AF:

0.00252

Gnomad AMR exome

AF:

0.0268

Gnomad ASJ exome

AF:

0.0199

Gnomad EAS exome

AF:

0.0578

Gnomad SAS exome

AF:

0.0321

Gnomad FIN exome

AF:

0.0203

Gnomad NFE exome

AF:

0.0128

Gnomad OTH exome

AF:

0.0191

GnomAD4 exome

AF:

0.0151

AC:

22010

AN:

1461734

Hom.:

274

Cov.:

AF XY:

0.0156

AC XY:

11318

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.00206

Gnomad4 AMR exome

AF:

0.0249

Gnomad4 ASJ exome

AF:

0.0181

Gnomad4 EAS exome

AF:

0.0621

Gnomad4 SAS exome

AF:

0.0317

Gnomad4 FIN exome

AF:

0.0200

Gnomad4 NFE exome

AF:

0.0117

Gnomad4 OTH exome

AF:

0.0176

GnomAD4 genome

AF:

0.0129

AC:

1960

AN:

152300

Hom.:

Cov.:

AF XY:

0.0144

AC XY:

1073

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00291

Gnomad4 AMR

AF:

0.0163

Gnomad4 ASJ

AF:

0.0184

Gnomad4 EAS

AF:

0.0631

Gnomad4 SAS

AF:

0.0390

Gnomad4 FIN

AF:

0.0207

Gnomad4 NFE

AF:

0.0112

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.0135

Hom.:

Bravo

AF:

0.0125

TwinsUK

AF:

0.0119

AC:

ALSPAC

AF:

0.0125

AC:

ESP6500AA

AF:

0.00364

AC:

ESP6500EA

AF:

0.0104

AC:

ExAC

AF:

0.0204

AC:

2474

Asia WGS

AF:

0.0590

AC:

203

AN:

3478

EpiCase

AF:

0.0113

EpiControl

AF:

0.0112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.025

.;T;.;.;T

Eigen

Benign

0.071

Eigen_PC

Benign

-0.013

FATHMM_MKL

Benign

0.65

LIST_S2

Uncertain

0.94

D;D;D;.;D

MetaRNN

Benign

0.0087

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

0.88

D;D;D;D;D;D;D

PrimateAI

Benign

0.41

PROVEAN

Benign

-2.1

N;N;N;N;N

REVEL

Benign

0.15

Sift

Uncertain

0.0010

D;D;D;D;D

Sift4G

Uncertain

0.0030

D;D;D;D;D

Vest4

0.22

MPC

0.83

ClinPred

0.021

GERP RS

3.0

gMVP

0.58

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over