Genetic Variant 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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007256.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2B1	NM_007256.5	MANE Select	c.-71T>C		5_prime_UTR	Exon 1 of 14	NP_009187.1
	SLCO2B1	NM_001145212.3		c.-71T>C		5_prime_UTR	Exon 1 of 11	NP_001138684.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLCO2B1	ENST00000289575.10	TSL:1 MANE Select	c.-71T>C	5_prime_UTR	Exon 1 of 14	ENSP00000289575.5
SLCO2B1	ENST00000531457.1	TSL:2	n.233T>C	non_coding_transcript_exon	Exon 1 of 2
SLCO2B1	ENST00000531756.5	TSL:2	n.242T>C	non_coding_transcript_exon	Exon 1 of 7

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over