dbSNP rs35199625: SLCO2B1:p.Val201Met (chr11-75169325-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

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

Publications

22 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLCO2B1	NM_007256.5 link	c.601G>A	p.Val201Met	missense_variant	Exon 5 of 14	ENST00000289575.10	NP_009187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000289575.10 link	c.601G>A	p.Val201Met	missense_variant	Exon 5 of 14	1	NM_007256.5	ENSP00000289575.5

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

GnomAD2 exomes

AF:

0.0208

AC:

5224

AN:

251208

AF XY:

0.0209

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 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

African (AFR)

AF:

0.00206

AC:

AN:

33480

American (AMR)

AF:

0.0249

AC:

1112

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0181

AC:

474

AN:

26134

East Asian (EAS)

AF:

0.0621

AC:

2464

AN:

39696

South Asian (SAS)

AF:

0.0317

AC:

2730

AN:

86244

European-Finnish (FIN)

AF:

0.0200

AC:

1070

AN:

53368

Middle Eastern (MID)

AF:

0.00711

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0117

AC:

12985

AN:

1111932

Other (OTH)

AF:

0.0176

AC:

1065

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

1219

2439

3658

4878

6097

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

542

1084

1626

2168

2710

<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

AF:

0.0129

AC:

1960

AN:

152300

Hom.:

Cov.:

AF XY:

0.0144

AC XY:

1073

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.00291

AC:

121

AN:

41566

American (AMR)

AF:

0.0163

AC:

249

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0184

AC:

AN:

3472

East Asian (EAS)

AF:

0.0631

AC:

326

AN:

5168

South Asian (SAS)

AF:

0.0390

AC:

188

AN:

4822

European-Finnish (FIN)

AF:

0.0207

AC:

220

AN:

10622

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0112

AC:

763

AN:

68026

Other (OTH)

AF:

0.0132

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

194

291

388

485

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0134

Hom.:

101

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

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0

.;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

MutationAssessor

Benign

0.0

.;.;.;.;.

PhyloP100

2.4

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

ClinPred

0.021

GERP RS

3.0

gMVP

0.58

Mutation Taster

=96/4

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over