dbSNP rs56027330: SLC17A3:p.Gly279Arg (chr6-25850617-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_001098486.2(SLC17A3):c.835G>A(p.Gly279Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,613,334 control chromosomes in the GnomAD database, including 11,020 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.090 ( 783 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10237 hom. )

Consequence

SLC17A3
NM_001098486.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.720

Variant links:

Genes affected

SLC17A3 (HGNC:10931): (solute carrier family 17 member 3) The protein encoded by this gene is a voltage-driven transporter that excretes intracellular urate and organic anions from the blood into renal tubule cells. Two transcript variants encoding different isoforms have been found for this gene. The longer isoform is a plasma membrane protein with transporter activity while the shorter isoform localizes to the endoplasmic reticulum. [provided by RefSeq, Aug 2012]

SLC17A3 links:

LOC124901285 (HGNC:):

LOC124901285 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 6-25850617-C-T is Benign according to our data. Variant chr6-25850617-C-T is described in ClinVar as [Benign]. Clinvar id is 3057092.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A3	NM_001098486.2 link	c.835G>A	p.Gly279Arg	missense_variant	Exon 8 of 13	ENST00000397060.8	NP_001091956.1	O00476-2
SLC17A3	NM_006632.4 link	c.601G>A	p.Gly201Arg	missense_variant	Exon 7 of 12		NP_006623.2	O00476-1A0A024QZX7
LOC124901285	XR_007059518.1 link	n.380-9029C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A3	ENST00000397060.8 link	c.835G>A	p.Gly279Arg	missense_variant	Exon 8 of 13	2	NM_001098486.2	ENSP00000380250.4		O00476-2

Frequencies

GnomAD3 genomes

AF:

0.0898

AC:

13655

AN:

152020

Hom.:

781

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0280

Gnomad AMI

AF:

0.0341

Gnomad AMR

AF:

0.0783

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.0201

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.105

AC:

26447

AN:

251326

Hom.:

1649

AF XY:

0.110

AC XY:

14937

AN XY:

135828

show subpopulations

Gnomad AFR exome

AF:

0.0274

Gnomad AMR exome

AF:

0.0730

Gnomad ASJ exome

AF:

0.128

Gnomad EAS exome

AF:

0.0244

Gnomad SAS exome

AF:

0.130

Gnomad FIN exome

AF:

0.132

Gnomad NFE exome

AF:

0.125

Gnomad OTH exome

AF:

0.112

GnomAD4 exome

AF:

0.115

AC:

167372

AN:

1461196

Hom.:

10237

Cov.:

AF XY:

0.116

AC XY:

84250

AN XY:

726938

show subpopulations

Gnomad4 AFR exome

AF:

0.0261

Gnomad4 AMR exome

AF:

0.0740

Gnomad4 ASJ exome

AF:

0.133

Gnomad4 EAS exome

AF:

0.0145

Gnomad4 SAS exome

AF:

0.131

Gnomad4 FIN exome

AF:

0.133

Gnomad4 NFE exome

AF:

0.120

Gnomad4 OTH exome

AF:

0.109

GnomAD4 genome

AF:

0.0898

AC:

13662

AN:

152138

Hom.:

783

Cov.:

AF XY:

0.0908

AC XY:

6749

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.0282

Gnomad4 AMR

AF:

0.0785

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.0195

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.134

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.116

Hom.:

1696

Bravo

AF:

0.0826

TwinsUK

AF:

0.114

AC:

421

ALSPAC

AF:

0.106

AC:

409

ESP6500AA

AF:

0.0327

AC:

144

ESP6500EA

AF:

0.126

AC:

1082

ExAC

AF:

0.106

AC:

12828

Asia WGS

AF:

0.0770

AC:

270

AN:

3478

EpiCase

AF:

0.122

EpiControl

AF:

0.119

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC17A3-related disorder

Benign:1

Nov 26, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.041

.;T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.0012

LIST_S2

Benign

0.064

T;.;T

MetaRNN

Benign

0.0015

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.66

.;N;N

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.25

N;N;N

REVEL

Benign

0.060

Sift

Benign

0.15

T;T;T

Sift4G

Benign

0.10

T;T;T

Polyphen

0.0

.;B;B

Vest4

0.070

MutPred

0.13

.;Gain of MoRF binding (P = 0.0132);Gain of MoRF binding (P = 0.0132);

MPC

0.034

ClinPred

0.0097

GERP RS

2.3

Varity_R

0.049

gMVP

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.28

Details are displayed if max score is > 0.2

DS_AL_spliceai

0.28

Position offset: 3

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