1-205920201-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_052934.4(SLC26A9):c.2085G>A(p.Val695=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0703 in 1,613,834 control chromosomes in the GnomAD database, including 4,294 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.070 ( 385 hom., cov: 32)

Exomes 𝑓: 0.070 ( 3909 hom. )

Consequence

SLC26A9
NM_052934.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.01

Variant links:

Genes affected

SLC26A9 (HGNC:14469): (solute carrier family 26 member 9) This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in their genomic (number and size of exons) and protein (aa length among species) structures yet have markedly different tissue expression patterns. The product of this gene is a highly selective chloride ion channel regulated by WNK kinases. Alternative splicing results in multiple transcript variants encoding differing isoforms.[provided by RefSeq, Dec 2008]

SLC26A9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 1-205920201-C-T is Benign according to our data. Variant chr1-205920201-C-T is described in ClinVar as [Benign]. Clinvar id is 403453.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SLC26A9	NM_052934.4 linkuse as main transcript	c.2085G>A	p.Val695=	synonymous_variant	18/21	ENST00000367135.8
SLC26A9	NM_134325.3 linkuse as main transcript	c.2085G>A	p.Val695=	synonymous_variant	18/22
SLC26A9	XM_011509121.3 linkuse as main transcript	c.1818G>A	p.Val606=	synonymous_variant	17/20
SLC26A9	XM_011509122.3 linkuse as main transcript	c.1593G>A	p.Val531=	synonymous_variant	15/18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC26A9	ENST00000367135.8 linkuse as main transcript	c.2085G>A	p.Val695=	synonymous_variant	18/21	1	NM_052934.4	P1	Q7LBE3-1
SLC26A9	ENST00000340781.8 linkuse as main transcript	c.2085G>A	p.Val695=	synonymous_variant	17/21	1			Q7LBE3-2
SLC26A9	ENST00000367134.2 linkuse as main transcript	c.2085G>A	p.Val695=	synonymous_variant	18/22	5			Q7LBE3-2
SLC26A9	ENST00000491127.5 linkuse as main transcript	n.1469G>A		non_coding_transcript_exon_variant	10/13	2

Frequencies

GnomAD3 genomes

AF:

0.0700

AC:

10653

AN:

152126

Hom.:

384

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0735

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.0631

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0317

Gnomad FIN

AF:

0.0425

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0772

Gnomad OTH

AF:

0.0936

GnomAD3 exomes

AF:

0.0626

AC:

15744

AN:

251478

Hom.:

621

AF XY:

0.0627

AC XY:

8527

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0773

Gnomad AMR exome

AF:

0.0446

Gnomad ASJ exome

AF:

0.130

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0323

Gnomad FIN exome

AF:

0.0462

Gnomad NFE exome

AF:

0.0803

Gnomad OTH exome

AF:

0.0813

GnomAD4 exome

AF:

0.0703

AC:

102798

AN:

1461590

Hom.:

3909

Cov.:

AF XY:

0.0700

AC XY:

50889

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.0713

Gnomad4 AMR exome

AF:

0.0465

Gnomad4 ASJ exome

AF:

0.130

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.0322

Gnomad4 FIN exome

AF:

0.0473

Gnomad4 NFE exome

AF:

0.0759

Gnomad4 OTH exome

AF:

0.0742

GnomAD4 genome

AF:

0.0700

AC:

10655

AN:

152244

Hom.:

385

Cov.:

AF XY:

0.0670

AC XY:

4987

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0734

Gnomad4 AMR

AF:

0.0629

Gnomad4 ASJ

AF:

0.133

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0317

Gnomad4 FIN

AF:

0.0425

Gnomad4 NFE

AF:

0.0773

Gnomad4 OTH

AF:

0.0931

Alfa

AF:

0.0805

Hom.:

873

Bravo

AF:

0.0733

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.0881

EpiControl

AF:

0.0901

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

Cadd

Benign

Dann

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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