Variant chr6-35944079-G-A 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_052961.4(SLC26A8):c.2734C>T(p.Pro912Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,614,056 control chromosomes in the GnomAD database, including 121 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0080 ( 7 hom., cov: 32)

Exomes 𝑓: 0.011 ( 114 hom. )

Consequence

SLC26A8
NM_052961.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.48

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:

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=0.003974676).

BP6

Variant 6-35944079-G-A is Benign according to our data. Variant chr6-35944079-G-A is described in ClinVar as [Benign]. Clinvar id is 2656511.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 1221 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC26A8	NM_052961.4 linkuse as main transcript	c.2734C>T	p.Pro912Ser	missense_variant	20/20	ENST00000490799.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC26A8	ENST00000490799.6 linkuse as main transcript	c.2734C>T	p.Pro912Ser	missense_variant	20/20	1	NM_052961.4	P1	Q96RN1-1

Frequencies

GnomAD3 genomes

AF:

0.00804

AC:

1222

AN:

152046

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00208

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.00603

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00872

Gnomad FIN

AF:

0.0172

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.00966

AC:

2429

AN:

251486

Hom.:

AF XY:

0.00995

AC XY:

1353

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.00209

Gnomad AMR exome

AF:

0.00491

Gnomad ASJ exome

AF:

0.00149

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00977

Gnomad FIN exome

AF:

0.0167

Gnomad NFE exome

AF:

0.0130

Gnomad OTH exome

AF:

0.0114

GnomAD4 exome

AF:

0.0111

AC:

16189

AN:

1461892

Hom.:

114

Cov.:

AF XY:

0.0109

AC XY:

7946

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.00164

Gnomad4 AMR exome

AF:

0.00541

Gnomad4 ASJ exome

AF:

0.00145

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.00996

Gnomad4 FIN exome

AF:

0.0178

Gnomad4 NFE exome

AF:

0.0119

Gnomad4 OTH exome

AF:

0.0119

GnomAD4 genome

AF:

0.00802

AC:

1221

AN:

152164

Hom.:

Cov.:

AF XY:

0.00776

AC XY:

577

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.00207

Gnomad4 AMR

AF:

0.00602

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00852

Gnomad4 FIN

AF:

0.0172

Gnomad4 NFE

AF:

0.0112

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.0104

Hom.:

Bravo

AF:

0.00728

TwinsUK

AF:

0.0119

AC:

ALSPAC

AF:

0.0109

AC:

ESP6500AA

AF:

0.00295

AC:

ESP6500EA

AF:

0.0117

AC:

101

ExAC

AF:

0.0103

AC:

1252

Asia WGS

AF:

0.00433

AC:

AN:

3478

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

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2024

SLC26A8: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.56

CADD

Benign

7.4

DANN

Benign

0.79

DEOGEN2

Benign

0.060

T;.;T

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.20

LIST_S2

Benign

0.47

.;T;T

MetaRNN

Benign

0.0040

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.0

M;.;M

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.25

PROVEAN

Benign

-1.9

N;N;N

REVEL

Benign

0.047

Sift

Benign

0.30

T;T;T

Sift4G

Uncertain

0.023

D;D;D

Polyphen

0.079

B;B;B

Vest4

0.23

MPC

0.70

ClinPred

0.0080

GERP RS

0.51

Varity_R

0.058

gMVP

0.27

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