dbSNP rs10770763: SLCO1B3-SLCO1B7:c.1865+64055T>C (chr12-20965522-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 ENST00000540229.1(SLCO1B3-SLCO1B7):c.1865+64055T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,698 control chromosomes in the GnomAD database, including 20,862 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 0.48 ( 20862 hom., cov: 32)

Consequence

SLCO1B3-SLCO1B7
ENST00000540229.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147

Publications

2 publications found

Variant links:

Genes affected

SLCO1B3-SLCO1B7 (HGNC:54403): (SLCO1B3-SLCO1B7 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring SLCO1B3 (solute carrier organic anion transporter family member 1B3) and SLCO1B7 (solute carrier organic anion transporter family member 1B7 (putative)) genes on chromosome 12. The readthrough transcript encodes a protein that shares sequence identity with both the upstream and downstream genes. [provided by RefSeq, Jun 2019]

SLCO1B3-SLCO1B7 links:

SLCO1B7 (HGNC:32934): (solute carrier organic anion transporter family member 1B7 (putative)) Predicted to enable bile acid transmembrane transporter activity and sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in bile acid and bile salt transport and sodium-independent organic anion transport. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLCO1B7 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

SLCO1B7 links:

LOC124902894 (HGNC:):

LOC124902894 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=-0.78).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO1B3-SLCO1B7	NM_001371097.1 link	c.1865+64055T>C		intron_variant	Intron 13 of 15		NP_001358026.1
LOC124902894	XM_047429949.1 link	c.-57-50117T>C		intron_variant	Intron 1 of 9		XP_047285905.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
SLCO1B3-SLCO1B7	ENST00000540229.1 link	c.1865+64055T>C	intron_variant	Intron 13 of 15	2	ENSP00000441269.1	A0A0A6YYJ9
SLCO1B3-SLCO1B7	ENST00000381541.7 link	c.360-55939T>C	intron_variant	Intron 3 of 13	2	ENSP00000370952.3	F5H094-1
SLCO1B7	ENST00000648739.1 link	n.84+2671T>C	intron_variant	Intron 1 of 13

Frequencies

GnomAD3 genomes

AF:

0.480

AC:

72732

AN:

151580

Hom.:

20854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.584

Gnomad AMR

AF:

0.532

Gnomad ASJ

AF:

0.525

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.741

Gnomad FIN

AF:

0.578

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.627

Gnomad OTH

AF:

0.489

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.480

AC:

72745

AN:

151698

Hom.:

20862

Cov.:

AF XY:

0.484

AC XY:

35870

AN XY:

74102

show subpopulations

African (AFR)

AF:

0.147

AC:

6115

AN:

41486

American (AMR)

AF:

0.532

AC:

8076

AN:

15170

Ashkenazi Jewish (ASJ)

AF:

0.525

AC:

1820

AN:

3466

East Asian (EAS)

AF:

0.554

AC:

2845

AN:

5134

South Asian (SAS)

AF:

0.742

AC:

3579

AN:

4826

European-Finnish (FIN)

AF:

0.578

AC:

6096

AN:

10550

Middle Eastern (MID)

AF:

0.555

AC:

162

AN:

292

European-Non Finnish (NFE)

AF:

0.627

AC:

42486

AN:

67758

Other (OTH)

AF:

0.491

AC:

1036

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1614

3229

4843

6458

8072

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.529

Hom.:

4129

Bravo

AF:

0.461

Asia WGS

AF:

0.604

AC:

2091

AN:

3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

4.9

(source)

DANN

Benign

0.92

PhyloP100

0.15

Mutation Taster

=100/0

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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rs10770763

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over