dbSNP rs2851069: SLCO2B1:c.-71T>C (chr11-75151311-T-C) – 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.-71T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 1,482,166 control chromosomes in the GnomAD database, including 248,504 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 19367 hom., cov: 32)

Exomes 𝑓: 0.58 ( 229137 hom. )

Consequence

SLCO2B1
NM_007256.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.549

Publications

23 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 (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO2B1	NM_007256.5 link	c.-71T>C		5_prime_UTR_variant	Exon 1 of 14	ENST00000289575.10	NP_009187.1
SLCO2B1	NM_001145212.3 link	c.-71T>C		5_prime_UTR_variant	Exon 1 of 11		NP_001138684.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000289575.10 link	c.-71T>C		5_prime_UTR_variant	Exon 1 of 14	1	NM_007256.5	ENSP00000289575.5

Frequencies

GnomAD3 genomes

AF:

0.471

AC:

71585

AN:

151986

Hom.:

19372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.537

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.651

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.617

Gnomad OTH

AF:

0.519

GnomAD4 exome

AF:

0.578

AC:

768213

AN:

1330062

Hom.:

229137

Cov.:

AF XY:

0.580

AC XY:

384880

AN XY:

664044

show subpopulations

African (AFR)

AF:

0.199

AC:

6163

AN:

30950

American (AMR)

AF:

0.336

AC:

13330

AN:

39680

Ashkenazi Jewish (ASJ)

AF:

0.552

AC:

13643

AN:

24708

East Asian (EAS)

AF:

0.217

AC:

8349

AN:

38432

South Asian (SAS)

AF:

0.549

AC:

43596

AN:

79470

European-Finnish (FIN)

AF:

0.640

AC:

32919

AN:

51458

Middle Eastern (MID)

AF:

0.566

AC:

3080

AN:

5446

European-Non Finnish (NFE)

AF:

0.614

AC:

616428

AN:

1003878

Other (OTH)

AF:

0.548

AC:

30705

AN:

56040

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

14970

29940

44909

59879

74849

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15856

31712

47568

63424

79280

<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:

0.471

AC:

71581

AN:

152104

Hom.:

19367

Cov.:

AF XY:

0.472

AC XY:

35120

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.212

AC:

8800

AN:

41500

American (AMR)

AF:

0.416

AC:

6360

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.537

AC:

1865

AN:

3470

East Asian (EAS)

AF:

0.239

AC:

1235

AN:

5164

South Asian (SAS)

AF:

0.543

AC:

2610

AN:

4810

European-Finnish (FIN)

AF:

0.651

AC:

6882

AN:

10578

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.617

AC:

41937

AN:

67970

Other (OTH)

AF:

0.515

AC:

1087

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1716

3432

5147

6863

8579

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<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:

0.558

Hom.:

97670

Bravo

AF:

0.439

Asia WGS

AF:

0.365

AC:

1274

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.4

(source)

DANN

Benign

0.54

PhyloP100

0.55

PromoterAI

-0.035

Neutral

(source)

Mutation Taster

=300/0

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