chr6-25842377-T-G

Position:

• chr6-25842377-T-G

Variant summary

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

The ENST00000481949.6(SLC17A3):​c.*2+3003A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,908 control chromosomes in the GnomAD database, including 20,884 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 0.52 (20884 hom., cov: 31)
• Consequence: SLC17A3 ENST00000481949.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901285	XR_007059518.1	n.379+5845T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A3	ENST00000481949.6	c.*2+3003A>C		intron_variant		3		ENSP00000421855.1
SLC17A3	ENST00000505420.5	c.*3-570A>C		intron_variant		5		ENSP00000424027.1

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78652 AN: 151788 Hom.: 20867 Cov.: 31

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.518 AC: 78713 AN: 151908 Hom.: 20884 Cov.: 31 AF XY: 0.524 AC XY: 38929 AN XY: 74250

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.527

Alfa AF: 0.513 Hom.: 29071

Bravo AF: 0.516

Asia WGS AF: 0.629 AC: 2189 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	5.5
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9393672; hg19: chr6-25842605; COSMIC: COSV62341599;