Variant rs2306168 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.1457C>T(p.Ser486Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 1,613,876 control chromosomes in the GnomAD database, including 7,253 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 0.13 ( 2574 hom., cov: 33)

Exomes 𝑓: 0.044 ( 4679 hom. )

Consequence

SLCO2B1
NM_007256.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.694

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:

SLCO2B1 (HGNC:):

SLCO2B1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0051302314).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO2B1	NM_007256.5 linkuse as main transcript	c.1457C>T	p.Ser486Phe	missense_variant	10/14	ENST00000289575.10	NP_009187.1	O94956A0A024R5I4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000289575.10 linkuse as main transcript	c.1457C>T	p.Ser486Phe	missense_variant	10/14	1	NM_007256.5	ENSP00000289575.5		A0A024R5I4

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19178

AN:

152124

Hom.:

2563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0991

Gnomad ASJ

AF:

0.0550

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.0631

Gnomad FIN

AF:

0.0374

Gnomad MID

AF:

0.0510

Gnomad NFE

AF:

0.0239

Gnomad OTH

AF:

0.101

GnomAD3 exomes

AF:

0.0775

AC:

19444

AN:

250876

Hom.:

1745

AF XY:

0.0696

AC XY:

9441

AN XY:

135656

show subpopulations

Gnomad AFR exome

AF:

0.340

Gnomad AMR exome

AF:

0.100

Gnomad ASJ exome

AF:

0.0542

Gnomad EAS exome

AF:

0.225

Gnomad SAS exome

AF:

0.0627

Gnomad FIN exome

AF:

0.0352

Gnomad NFE exome

AF:

0.0245

Gnomad OTH exome

AF:

0.0554

GnomAD4 exome

AF:

0.0443

AC:

64681

AN:

1461634

Hom.:

4679

Cov.:

AF XY:

0.0435

AC XY:

31604

AN XY:

727122

show subpopulations

Gnomad4 AFR exome

AF:

0.343

Gnomad4 AMR exome

AF:

0.100

Gnomad4 ASJ exome

AF:

0.0517

Gnomad4 EAS exome

AF:

0.276

Gnomad4 SAS exome

AF:

0.0626

Gnomad4 FIN exome

AF:

0.0356

Gnomad4 NFE exome

AF:

0.0225

Gnomad4 OTH exome

AF:

0.0640

GnomAD4 genome

AF:

0.126

AC:

19230

AN:

152242

Hom.:

2574

Cov.:

AF XY:

0.126

AC XY:

9384

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.329

Gnomad4 AMR

AF:

0.0992

Gnomad4 ASJ

AF:

0.0550

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.0633

Gnomad4 FIN

AF:

0.0374

Gnomad4 NFE

AF:

0.0239

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.0460

Hom.:

677

Bravo

AF:

0.140

TwinsUK

AF:

0.0208

AC:

ALSPAC

AF:

0.0208

AC:

ESP6500AA

AF:

0.331

AC:

1457

ESP6500EA

AF:

0.0254

AC:

218

ExAC

AF:

0.0802

AC:

9732

Asia WGS

AF:

0.176

AC:

610

AN:

3478

EpiCase

AF:

0.0254

EpiControl

AF:

0.0256

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.091

DEOGEN2

Benign

0.0019

.;T;.;.;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.027

LIST_S2

Benign

0.47

T;T;T;.;.

MetaRNN

Benign

0.0051

T;T;T;T;T

MetaSVM

Benign

-0.95

PrimateAI

Benign

0.44

PROVEAN

Benign

1.8

N;N;N;N;N

REVEL

Benign

0.022

Sift

Benign

0.71

T;T;T;T;T

Sift4G

Benign

0.72

T;T;T;T;T

Vest4

0.12

MPC

0.25

ClinPred

0.0014

GERP RS

3.0

gMVP

0.54

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