dbSNP rs2417873: SLCO1B3-SLCO1B7:c.1866-53930G>A (chr12-21013389-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 ENST00000540229.1(SLCO1B3-SLCO1B7):c.1866-53930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,128 control chromosomes in the GnomAD database, including 15,681 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 0.39 ( 15681 hom., cov: 32)

Consequence

SLCO1B3-SLCO1B7
ENST00000540229.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

Publications

5 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO1B3-SLCO1B7	NM_001371097.1 link	c.1866-53930G>A		intron_variant	Intron 13 of 15		NP_001358026.1
LOC124902894	XM_047429949.1 link	c.-57-2250G>A		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.1866-53930G>A	intron_variant	Intron 13 of 15	2	ENSP00000441269.1	A0A0A6YYJ9
SLCO1B3-SLCO1B7	ENST00000381541.7 link	c.360-8072G>A	intron_variant	Intron 3 of 13	2	ENSP00000370952.3	F5H094-1
SLCO1B7	ENST00000648739.1 link	n.85-2250G>A	intron_variant	Intron 1 of 13

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59409

AN:

152010

Hom.:

15639

Cov.:

show subpopulations

Gnomad AFR

AF:

0.753

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.162

Gnomad SAS

AF:

0.168

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.261

Gnomad OTH

AF:

0.376

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

GnomAD4 genome

AF:

0.391

AC:

59501

AN:

152128

Hom.:

15681

Cov.:

AF XY:

0.379

AC XY:

28166

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.753

AC:

31262

AN:

41490

American (AMR)

AF:

0.294

AC:

4491

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

1311

AN:

3468

East Asian (EAS)

AF:

0.162

AC:

841

AN:

5178

South Asian (SAS)

AF:

0.167

AC:

807

AN:

4828

European-Finnish (FIN)

AF:

0.179

AC:

1898

AN:

10578

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.261

AC:

17765

AN:

67994

Other (OTH)

AF:

0.375

AC:

791

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1475

2950

4424

5899

7374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<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:

0.310

Hom.:

29816

Bravo

AF:

0.417

Asia WGS

AF:

0.220

AC:

765

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.3

(source)

DANN

Benign

0.30

PhyloP100

0.055

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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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