Variant 6-35992613-C-T 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.689G>A(p.Ser230Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,613,622 control chromosomes in the GnomAD database, including 12,785 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 0.10 ( 940 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11845 hom. )

Consequence

SLC26A8
NM_052961.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.156

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:

LOC105375035 (HGNC:):

LOC105375035 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0041314363).

BP6

Variant 6-35992613-C-T is Benign according to our data. Variant chr6-35992613-C-T is described in ClinVar as [Benign]. Clinvar id is 1243863.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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.689G>A	p.Ser230Asn	missense_variant	6/20	ENST00000490799.6
LOC105375035	XR_926747.3 linkuse as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC26A8	ENST00000490799.6 linkuse as main transcript	c.689G>A	p.Ser230Asn	missense_variant	6/20	1	NM_052961.4	P1	Q96RN1-1
SLC26A8	ENST00000394602.6 linkuse as main transcript	c.627+5125G>A		intron_variant		1			Q96RN1-2
SLC26A8	ENST00000355574.6 linkuse as main transcript	c.689G>A	p.Ser230Asn	missense_variant	6/20	2		P1	Q96RN1-1
SLC26A8	ENST00000486155.1 linkuse as main transcript	n.1044G>A		non_coding_transcript_exon_variant	6/13	2

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15932

AN:

152110

Hom.:

939

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0438

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.0549

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.128

GnomAD3 exomes

AF:

0.120

AC:

29994

AN:

250822

Hom.:

2031

AF XY:

0.122

AC XY:

16487

AN XY:

135580

show subpopulations

Gnomad AFR exome

AF:

0.0390

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.227

Gnomad EAS exome

AF:

0.0552

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.131

Gnomad NFE exome

AF:

0.132

Gnomad OTH exome

AF:

0.131

GnomAD4 exome

AF:

0.123

AC:

179702

AN:

1461394

Hom.:

11845

Cov.:

AF XY:

0.123

AC XY:

89614

AN XY:

726998

show subpopulations

Gnomad4 AFR exome

AF:

0.0385

Gnomad4 AMR exome

AF:

0.119

Gnomad4 ASJ exome

AF:

0.232

Gnomad4 EAS exome

AF:

0.0484

Gnomad4 SAS exome

AF:

0.113

Gnomad4 FIN exome

AF:

0.132

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.105

AC:

15935

AN:

152228

Hom.:

940

Cov.:

AF XY:

0.105

AC XY:

7809

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0437

Gnomad4 AMR

AF:

0.113

Gnomad4 ASJ

AF:

0.238

Gnomad4 EAS

AF:

0.0550

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.127

Alfa

AF:

0.131

Hom.:

3066

Bravo

AF:

0.102

TwinsUK

AF:

0.130

AC:

481

ALSPAC

AF:

0.121

AC:

467

ESP6500AA

AF:

0.0427

AC:

188

ESP6500EA

AF:

0.133

AC:

1143

ExAC

AF:

0.118

AC:

14348

Asia WGS

AF:

0.0770

AC:

267

AN:

3478

EpiCase

AF:

0.141

EpiControl

AF:

0.133

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

Jun 09, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.42

CADD

Benign

4.7

DANN

Benign

0.16

DEOGEN2

Benign

0.37

T;T

Eigen

Benign

-0.69

Eigen_PC

Benign

-0.63

FATHMM_MKL

Benign

0.062

LIST_S2

Benign

0.62

.;T

MetaRNN

Benign

0.0041

T;T

MetaSVM

Benign

-0.71

MutationAssessor

Benign

0.89

L;L

MutationTaster

Benign

0.95

P;P;P

PrimateAI

Benign

0.32

PROVEAN

Benign

-0.32

N;N

REVEL

Benign

0.18

Sift

Benign

0.27

T;T

Sift4G

Benign

0.28

T;T

Polyphen

0.031

B;B

Vest4

0.032

MPC

0.21

ClinPred

0.0043

GERP RS

3.3

Varity_R

0.073

gMVP

0.56

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