rs942379

chr6-25849392-A-Gchr6-25849392-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001098486.2(SLC17A3):c.1344T>C(p.Ser448=) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

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]

LOC124901285 (HGNC:):

ACMG classification

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	UniProt
SLC17A3	NM_001098486.2	c.1344T>C	p.Ser448=	synonymous_variant	11/13	ENST00000397060.8
LOC124901285	XR_007059518.1	n.380-10254A>G		intron_variant, non_coding_transcript_variant
SLC17A3	NM_006632.4	c.1110T>C	p.Ser370=	synonymous_variant	10/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A3	ENST00000397060.8	c.1344T>C	p.Ser448=	synonymous_variant	11/13	2	NM_001098486.2	P1

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98153 AN: 151820 Hom.: 33543 Cov.: 31

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

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.: 31 AF XY: 0.558 AC XY: 403731 AN XY: 723276

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.: 31 AF XY: 0.647 AC XY: 47999 AN XY: 74242

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

Other links and lift over

dbSNP: rs942379; hg19: chr6-25849620; COSMIC: COSV57761341; COSMIC: COSV57761341;