rs1165205

Positions:

• chr6-25870314-T-A
• chr6-25870314-T-C
• chr6-25870314-T-G

Variant summary

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

The NM_001098486.2(SLC17A3):​c.-33-1894A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,880 control chromosomes in the GnomAD database, including 33,167 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 0.64 (33167 hom., cov: 31)
• Consequence: SLC17A3 NM_001098486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A3	NM_001098486.2	c.-33-1894A>T		intron_variant		ENST00000397060.8	NP_001091956.1
SLC17A3	NM_006632.4	c.-33-1894A>T		intron_variant			NP_006623.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A3	ENST00000397060.8	c.-33-1894A>T		intron_variant		2	NM_001098486.2	ENSP00000380250	P1

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97265 AN: 151762 Hom.: 33109 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.645

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.641 AC: 97383 AN: 151880 Hom.: 33167 Cov.: 31 AF XY: 0.640 AC XY: 47516 AN XY: 74238

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.644

Alfa AF: 0.552 Hom.: 13026

Bravo AF: 0.658

Asia WGS AF: 0.658 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.73

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: rs1165205; hg19: chr6-25870542;