Variant rs942379 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001098486.2(SLC17A3):c.1344T>C(p.Ser448Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 1,604,642 control chromosomes in the GnomAD database, including 269,051 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 33604 hom., cov: 31)

Exomes 𝑓: 0.56 ( 235447 hom. )

Consequence

SLC17A3
NM_001098486.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=-0.632 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A3	NM_001098486.2 linkuse as main transcript	c.1344T>C	p.Ser448Ser	synonymous_variant	11/13	ENST00000397060.8	NP_001091956.1	O00476-2
SLC17A3	NM_006632.4 linkuse as main transcript	c.1110T>C	p.Ser370Ser	synonymous_variant	10/12		NP_006623.2	O00476-1A0A024QZX7
LOC124901285	XR_007059518.1 linkuse as main transcript	n.380-10254A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A3	ENST00000397060.8 linkuse as main transcript	c.1344T>C	p.Ser448Ser	synonymous_variant	11/13	2	NM_001098486.2	ENSP00000380250.4		O00476-2

Frequencies

GnomAD3 genomes

AF:

0.647

AC:

98153

AN:

151820

Hom.:

33543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.866

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.645

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.828

Gnomad SAS

AF:

0.501

Gnomad FIN

AF:

0.597

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.532

Gnomad OTH

AF:

0.646

GnomAD3 exomes

AF:

0.600

AC:

150403

AN:

250766

Hom.:

47299

AF XY:

0.583

AC XY:

79004

AN XY:

135540

show subpopulations

Gnomad AFR exome

AF:

0.874

Gnomad AMR exome

AF:

0.713

Gnomad ASJ exome

AF:

0.457

Gnomad EAS exome

AF:

0.857

Gnomad SAS exome

AF:

0.498

Gnomad FIN exome

AF:

0.587

Gnomad NFE exome

AF:

0.529

Gnomad OTH exome

AF:

0.559

GnomAD4 exome

AF:

0.563

AC:

817517

AN:

1452704

Hom.:

235447

Cov.:

AF XY:

0.558

AC XY:

403731

AN XY:

723276

show subpopulations

Gnomad4 AFR exome

AF:

0.885

Gnomad4 AMR exome

AF:

0.701

Gnomad4 ASJ exome

AF:

0.467

Gnomad4 EAS exome

AF:

0.843

Gnomad4 SAS exome

AF:

0.502

Gnomad4 FIN exome

AF:

0.586

Gnomad4 NFE exome

AF:

0.542

Gnomad4 OTH exome

AF:

0.579

GnomAD4 genome

AF:

0.647

AC:

98277

AN:

151938

Hom.:

33604

Cov.:

AF XY:

0.647

AC XY:

47999

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.867

Gnomad4 AMR

AF:

0.646

Gnomad4 ASJ

AF:

0.449

Gnomad4 EAS

AF:

0.827

Gnomad4 SAS

AF:

0.501

Gnomad4 FIN

AF:

0.597

Gnomad4 NFE

AF:

0.532

Gnomad4 OTH

AF:

0.646

Alfa

AF:

0.534

Hom.:

35087

Bravo

AF:

0.667

Asia WGS

AF:

0.663

AC:

2307

AN:

3478

EpiCase

AF:

0.525

EpiControl

AF:

0.515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.54

DANN

Benign

0.54

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over