Variant rs2295852 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_052961.4(SLC26A8):c.1915A>G(p.Ile639Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 1,613,794 control chromosomes in the GnomAD database, including 107,216 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.42 ( 15087 hom., cov: 31)

Exomes 𝑓: 0.35 ( 92129 hom. )

Consequence

SLC26A8
NM_052961.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.34

Variant links:

Genes affected

SLC26A8 (HGNC:14468): (solute carrier family 26 member 8) This gene encodes a member of the SLC26 gene family of anion transporters. Family members are well conserved in gene structure and protein length yet have markedly different tissue expression patterns. The expression of this gene appears to be restricted to spermatocytes. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Jul 2010]

SLC26A8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.815994E-6).

BP6

Variant 6-35955469-T-C is Benign according to our data. Variant chr6-35955469-T-C is described in ClinVar as [Benign]. Clinvar id is 1234924.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC26A8	NM_052961.4 linkuse as main transcript	c.1915A>G	p.Ile639Val	missense_variant	17/20	ENST00000490799.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC26A8	ENST00000490799.6 linkuse as main transcript	c.1915A>G	p.Ile639Val	missense_variant	17/20	1	NM_052961.4	P1	Q96RN1-1

Frequencies

GnomAD3 genomes

AF:

0.420

AC:

63777

AN:

151864

Hom.:

15044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.646

Gnomad AMI

AF:

0.407

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.308

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.428

GnomAD3 exomes

AF:

0.335

AC:

84110

AN:

251336

Hom.:

15475

AF XY:

0.333

AC XY:

45172

AN XY:

135832

show subpopulations

Gnomad AFR exome

AF:

0.650

Gnomad AMR exome

AF:

0.215

Gnomad ASJ exome

AF:

0.324

Gnomad EAS exome

AF:

0.296

Gnomad SAS exome

AF:

0.285

Gnomad FIN exome

AF:

0.315

Gnomad NFE exome

AF:

0.350

Gnomad OTH exome

AF:

0.345

GnomAD4 exome

AF:

0.349

AC:

510559

AN:

1461812

Hom.:

92129

Cov.:

AF XY:

0.346

AC XY:

251855

AN XY:

727204

show subpopulations

Gnomad4 AFR exome

AF:

0.656

Gnomad4 AMR exome

AF:

0.230

Gnomad4 ASJ exome

AF:

0.325

Gnomad4 EAS exome

AF:

0.280

Gnomad4 SAS exome

AF:

0.283

Gnomad4 FIN exome

AF:

0.318

Gnomad4 NFE exome

AF:

0.354

Gnomad4 OTH exome

AF:

0.356

GnomAD4 genome

AF:

0.420

AC:

63863

AN:

151982

Hom.:

15087

Cov.:

AF XY:

0.414

AC XY:

30730

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.647

Gnomad4 AMR

AF:

0.323

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.295

Gnomad4 SAS

AF:

0.291

Gnomad4 FIN

AF:

0.308

Gnomad4 NFE

AF:

0.345

Gnomad4 OTH

AF:

0.429

Alfa

AF:

0.360

Hom.:

26053

Bravo

AF:

0.435

TwinsUK

AF:

0.357

AC:

1324

ALSPAC

AF:

0.361

AC:

1390

ESP6500AA

AF:

0.637

AC:

2807

ESP6500EA

AF:

0.349

AC:

3003

ExAC

AF:

0.346

AC:

41971

Asia WGS

AF:

0.309

AC:

1074

AN:

3478

EpiCase

AF:

0.359

EpiControl

AF:

0.358

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.37

CADD

Benign

0.0010

DANN

Benign

0.28

DEOGEN2

Benign

0.096

T;.;T

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.014

LIST_S2

Benign

0.25

.;T;T

MetaRNN

Benign

0.0000028

T;T;T

MetaSVM

Benign

-0.57

MutationAssessor

Benign

0.46

N;.;N

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.020

N;N;N

REVEL

Benign

0.21

Sift

Benign

0.98

T;T;T

Sift4G

Benign

0.41

T;T;T

Polyphen

0.0

B;B;B

Vest4

0.028

MPC

0.18

ClinPred

0.00059

GERP RS

-5.0

Varity_R

0.023

gMVP

0.37

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over