rs942379

Variant names:

• chr6-25849392-A-G
• rs942379
• NM_001098486.2:c.1344T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-25849392-A-G
• chr6-25849392-A-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 32 publications found

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

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.006).
• 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 rank	MANE	Protein	UniProt
SLC17A3	NM_001098486.2	c.1344T>C	p.Ser448Ser	synonymous_variant	Exon 11 of 13	ENST00000397060.8	NP_001091956.1
SLC17A3	NM_006632.4	c.1110T>C	p.Ser370Ser	synonymous_variant	Exon 10 of 12		NP_006623.2
LOC124901285	XR_007059518.1	n.380-10254A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A3	ENST00000397060.8	c.1344T>C	p.Ser448Ser	synonymous_variant	Exon 11 of 13	2	NM_001098486.2	ENSP00000380250.4

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

GnomAD2 exomes AF: 0.600 AC: 150403 AN: 250766 AF XY: 0.583

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 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

African (AFR) AF: 0.885 AC: 29415 AN: 33238

American (AMR) AF: 0.701 AC: 31354 AN: 44700

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 12170 AN: 26054

East Asian (EAS) AF: 0.843 AC: 33402 AN: 39628

South Asian (SAS) AF: 0.502 AC: 43201 AN: 86014

European-Finnish (FIN) AF: 0.586 AC: 31307 AN: 53390

Middle Eastern (MID) AF: 0.545 AC: 3129 AN: 5742

European-Non Finnish (NFE) AF: 0.542 AC: 598712 AN: 1103838

Other (OTH) AF: 0.579 AC: 34827 AN: 60100

GnomAD4 genome AF: 0.647 AC: 98277 AN: 151938 Hom.: 33604 Cov.: 31 AF XY: 0.647 AC XY: 47999 AN XY: 74242

African (AFR) AF: 0.867 AC: 35959 AN: 41488

American (AMR) AF: 0.646 AC: 9861 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4272 AN: 5166

South Asian (SAS) AF: 0.501 AC: 2405 AN: 4800

European-Finnish (FIN) AF: 0.597 AC: 6274 AN: 10508

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36132 AN: 67928

Other (OTH) AF: 0.646 AC: 1362 AN: 2108

Alfa AF: 0.554 Hom.: 52796

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
PhyloP100		-0.63
PromoterAI		-0.00060	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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