rs13198474

Positions:

• chr6-25874195-G-A
• chr6-25874195-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001098486.2(SLC17A3):​c.-62C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,224 control chromosomes in the GnomAD database, including 173 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 0.039 (173 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: SLC17A3 NM_001098486.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A3	NM_001098486.2	c.-62C>T		5_prime_UTR_variant	1/13	ENST00000397060.8	NP_001091956.1
SLC17A3	NM_006632.4	c.-62C>T		5_prime_UTR_variant	1/12		NP_006623.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A3	ENST00000397060.8	c.-62C>T		5_prime_UTR_variant	1/13	2	NM_001098486.2	ENSP00000380250	P1

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5966 AN: 152098 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0244

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0392 AC: 5961 AN: 152216 Hom.: 173 Cov.: 32 AF XY: 0.0356 AC XY: 2652 AN XY: 74414

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0171

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0699

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0608 Hom.: 270

Bravo AF: 0.0364

Asia WGS AF: 0.00375 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.44

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: rs13198474; hg19: chr6-25874423;