3-48628021-G-A

Variant summary

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

The NM_022911.3(SLC26A6):​c.1818C>T​(p.Gly606=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00305 in 1,580,388 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0032 ( 8 hom. )

Consequence

SLC26A6
NM_022911.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.02
Variant links:
Genes affected
SLC26A6 (HGNC:14472): (solute carrier family 26 member 6) This gene belongs to the solute carrier 26 family, whose members encode anion transporter proteins. This particular family member encodes a protein involved in transporting chloride, oxalate, sulfate and bicarbonate. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Aug 2013]

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=-0.8).
BP6
Variant 3-48628021-G-A is Benign according to our data. Variant chr3-48628021-G-A is described in ClinVar as [Benign]. Clinvar id is 782985.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.02 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC26A6NM_022911.3 linkuse as main transcriptc.1818C>T p.Gly606= synonymous_variant 17/21 ENST00000395550.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC26A6ENST00000395550.7 linkuse as main transcriptc.1818C>T p.Gly606= synonymous_variant 17/211 NM_022911.3 P4Q9BXS9-1

Frequencies

GnomAD3 genomes
AF:
0.00198
AC:
301
AN:
152170
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000555
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00443
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00318
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00285
AC:
619
AN:
217350
Hom.:
1
AF XY:
0.00286
AC XY:
340
AN XY:
119040
show subpopulations
Gnomad AFR exome
AF:
0.000898
Gnomad AMR exome
AF:
0.000571
Gnomad ASJ exome
AF:
0.000236
Gnomad EAS exome
AF:
0.0000654
Gnomad SAS exome
AF:
0.0000404
Gnomad FIN exome
AF:
0.00469
Gnomad NFE exome
AF:
0.00463
Gnomad OTH exome
AF:
0.00176
GnomAD4 exome
AF:
0.00316
AC:
4513
AN:
1428100
Hom.:
8
Cov.:
31
AF XY:
0.00307
AC XY:
2181
AN XY:
709858
show subpopulations
Gnomad4 AFR exome
AF:
0.000574
Gnomad4 AMR exome
AF:
0.000517
Gnomad4 ASJ exome
AF:
0.000282
Gnomad4 EAS exome
AF:
0.0000522
Gnomad4 SAS exome
AF:
0.0000373
Gnomad4 FIN exome
AF:
0.00455
Gnomad4 NFE exome
AF:
0.00369
Gnomad4 OTH exome
AF:
0.00268
GnomAD4 genome
AF:
0.00197
AC:
300
AN:
152288
Hom.:
0
Cov.:
32
AF XY:
0.00197
AC XY:
147
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.000553
Gnomad4 AMR
AF:
0.000457
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00443
Gnomad4 NFE
AF:
0.00316
Gnomad4 OTH
AF:
0.00236
Alfa
AF:
0.00267
Hom.:
0
Bravo
AF:
0.00204

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 submitterclinical testingInvitaeMar 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
9.0
DANN
Benign
0.40
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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.

Other links and lift over

dbSNP: rs199596871; hg19: chr3-48665454; COSMIC: COSV56570585; COSMIC: COSV56570585; API