Variant chr11-63297692-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001039752.4(SLC22A10):c.795G>A(p.Ala265=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00437 in 1,613,946 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0044 ( 29 hom. )

Consequence

SLC22A10
NM_001039752.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.44

Variant links:

Genes affected

SLC22A10 (HGNC:18057): (solute carrier family 22 member 10) Predicted to enable transmembrane transporter activity. Predicted to be involved in organic anion transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC22A10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 11-63297692-G-A is Benign according to our data. Variant chr11-63297692-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2641899.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.44 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 29 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A10	NM_001039752.4 linkuse as main transcript	c.795G>A	p.Ala265=	synonymous_variant	4/10	ENST00000332793.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A10	ENST00000332793.11 linkuse as main transcript	c.795G>A	p.Ala265=	synonymous_variant	4/10	1	NM_001039752.4	P1	Q63ZE4-1

Frequencies

GnomAD3 genomes

AF:

0.00415

AC:

632

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000773

Gnomad AMI

AF:

0.0559

Gnomad AMR

AF:

0.00340

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.00876

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00519

Gnomad OTH

AF:

0.00384

GnomAD3 exomes

AF:

0.00455

AC:

1134

AN:

249040

Hom.:

AF XY:

0.00482

AC XY:

651

AN XY:

135120

show subpopulations

Gnomad AFR exome

AF:

0.000581

Gnomad AMR exome

AF:

0.00235

Gnomad ASJ exome

AF:

0.00845

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.00520

Gnomad FIN exome

AF:

0.00840

Gnomad NFE exome

AF:

0.00522

Gnomad OTH exome

AF:

0.00464

GnomAD4 exome

AF:

0.00440

AC:

6426

AN:

1461706

Hom.:

Cov.:

AF XY:

0.00459

AC XY:

3341

AN XY:

727148

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00264

Gnomad4 ASJ exome

AF:

0.00922

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00552

Gnomad4 FIN exome

AF:

0.00796

Gnomad4 NFE exome

AF:

0.00429

Gnomad4 OTH exome

AF:

0.00475

GnomAD4 genome

AF:

0.00416

AC:

633

AN:

152240

Hom.:

Cov.:

AF XY:

0.00438

AC XY:

326

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.000794

Gnomad4 AMR

AF:

0.00340

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00395

Gnomad4 FIN

AF:

0.00876

Gnomad4 NFE

AF:

0.00519

Gnomad4 OTH

AF:

0.00380

Alfa

AF:

0.00480

Hom.:

Bravo

AF:

0.00395

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.00638

EpiControl

AF:

0.00741

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

SLC22A10: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.4

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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