rs548987

Positions:

• chr6-25869143-G-C

Variant summary

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

The NM_001098486.2(SLC17A3):​c.-33-723C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,888 control chromosomes in the GnomAD database, including 4,223 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 0.20 (4223 hom., cov: 32)
• Consequence: SLC17A3 NM_001098486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A3	NM_001098486.2	c.-33-723C>G		intron_variant		ENST00000397060.8
SLC17A3	NM_006632.4	c.-33-723C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A3	ENST00000397060.8	c.-33-723C>G		intron_variant		2	NM_001098486.2	P1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29727 AN: 151770 Hom.: 4216 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.196 AC: 29750 AN: 151888 Hom.: 4223 Cov.: 32 AF XY: 0.191 AC XY: 14203 AN XY: 74234

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0631

Gnomad4 FIN AF: 0.0847

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.185

Alfa AF: 0.169 Hom.: 381

Bravo AF: 0.213

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.37

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: rs548987; hg19: chr6-25869371;