Variant 15-92147149-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_013272.4(SLCO3A1):c.1678A>G(p.Ile560Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0036 in 1,611,904 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 14 hom. )

Consequence

SLCO3A1
NM_013272.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 8.73

Variant links:

Genes affected

SLCO3A1 (HGNC:10952): (solute carrier organic anion transporter family member 3A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Involved in positive regulation of NF-kappaB transcription factor activity; positive regulation of protein phosphorylation; and prostaglandin transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLCO3A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013807863).

BP6

Variant 15-92147149-A-G is Benign according to our data. Variant chr15-92147149-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2645719.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 14 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLCO3A1	NM_013272.4 linkuse as main transcript	c.1678A>G	p.Ile560Val	missense_variant	8/10	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1 linkuse as main transcript	c.1678A>G	p.Ile560Val	missense_variant	8/11		NP_001138516.1
SLCO3A1	NR_135775.2 linkuse as main transcript	n.1605A>G		non_coding_transcript_exon_variant	8/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11 linkuse as main transcript	c.1678A>G	p.Ile560Val	missense_variant	8/10	1	NM_013272.4	ENSP00000320634	P1	Q9UIG8-1

Frequencies

GnomAD3 genomes

AF:

0.00221

AC:

335

AN:

151398

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000735

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000787

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.00208

Gnomad FIN

AF:

0.000755

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00399

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00212

AC:

528

AN:

249424

Hom.:

AF XY:

0.00226

AC XY:

304

AN XY:

134772

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.000378

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00296

Gnomad FIN exome

AF:

0.000232

Gnomad NFE exome

AF:

0.00355

Gnomad OTH exome

AF:

0.00132

GnomAD4 exome

AF:

0.00375

AC:

5475

AN:

1460392

Hom.:

Cov.:

AF XY:

0.00370

AC XY:

2685

AN XY:

726516

show subpopulations

Gnomad4 AFR exome

AF:

0.000601

Gnomad4 AMR exome

AF:

0.000404

Gnomad4 ASJ exome

AF:

0.0000769

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00297

Gnomad4 FIN exome

AF:

0.000487

Gnomad4 NFE exome

AF:

0.00444

Gnomad4 OTH exome

AF:

0.00338

GnomAD4 genome

AF:

0.00221

AC:

335

AN:

151512

Hom.:

Cov.:

AF XY:

0.00217

AC XY:

161

AN XY:

74076

show subpopulations

Gnomad4 AFR

AF:

0.000733

Gnomad4 AMR

AF:

0.000786

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00208

Gnomad4 FIN

AF:

0.000755

Gnomad4 NFE

AF:

0.00399

Gnomad4 OTH

AF:

0.00143

Alfa

AF:

0.00320

Hom.:

Bravo

AF:

0.00213

TwinsUK

AF:

0.00566

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.000910

AC:

ESP6500EA

AF:

0.00337

AC:

ExAC

AF:

0.00216

AC:

262

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00382

EpiControl

AF:

0.00320

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

SLCO3A1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.054

T;.

Eigen

Uncertain

0.26

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.91

D;D

M_CAP

Benign

0.0072

MetaRNN

Benign

0.014

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.41

N;N

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

-0.60

N;N

REVEL

Benign

0.18

Sift

Benign

0.68

T;T

Sift4G

Benign

0.26

T;T

Polyphen

0.75

P;D

Vest4

0.62

MVP

0.043

MPC

0.44

ClinPred

0.045

GERP RS

6.0

Varity_R

0.22

gMVP

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over