Variant rs2851069 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.-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

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 (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/exons	MANE	Protein	UniProt
SLCO2B1	NM_007256.5 linkuse as main transcript	c.-71T>C		5_prime_UTR_variant	1/14	ENST00000289575.10	NP_009187.1
SLCO2B1	NM_001145212.3 linkuse as main transcript	c.-71T>C		5_prime_UTR_variant	1/11		NP_001138684.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000289575.10 linkuse as main transcript	c.-71T>C		5_prime_UTR_variant	1/14	1	NM_007256.5	ENSP00000289575	P2

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

Gnomad4 AFR exome

AF:

0.199

Gnomad4 AMR exome

AF:

0.336

Gnomad4 ASJ exome

AF:

0.552

Gnomad4 EAS exome

AF:

0.217

Gnomad4 SAS exome

AF:

0.549

Gnomad4 FIN exome

AF:

0.640

Gnomad4 NFE exome

AF:

0.614

Gnomad4 OTH exome

AF:

0.548

GnomAD4 genome

AF:

0.471

AC:

71581

AN:

152104

Hom.:

19367

Cov.:

AF XY:

0.472

AC XY:

35120

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.416

Gnomad4 ASJ

AF:

0.537

Gnomad4 EAS

AF:

0.239

Gnomad4 SAS

AF:

0.543

Gnomad4 FIN

AF:

0.651

Gnomad4 NFE

AF:

0.617

Gnomad4 OTH

AF:

0.515

Alfa

AF:

0.586

Hom.:

43778

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

DANN

Benign

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