chr6-25873518-C-A

Position:

• chr6-25873518-C-A

Variant summary

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

The NM_001098486.2(SLC17A3):​c.-34+649G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0713 in 152,126 control chromosomes in the GnomAD database, including 423 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 0.071 (423 hom., cov: 31)
• Consequence: SLC17A3 NM_001098486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A3	NM_001098486.2	c.-34+649G>T		intron_variant		ENST00000397060.8
SLC17A3	NM_006632.4	c.-34+649G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A3	ENST00000397060.8	c.-34+649G>T		intron_variant		2	NM_001098486.2	P1

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10851 AN: 152008 Hom.: 424 Cov.: 31

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.0155

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0713 AC: 10850 AN: 152126 Hom.: 423 Cov.: 31 AF XY: 0.0671 AC XY: 4994 AN XY: 74390

Gnomad4 AFR AF: 0.0802

Gnomad4 AMR AF: 0.0521

Gnomad4 ASJ AF: 0.0306

Gnomad4 EAS AF: 0.0154

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0867

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0808 Hom.: 510

Bravo AF: 0.0745

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.72

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: rs9467626; hg19: chr6-25873746;