6-25842723-T-G

Variant names:

• chr6-25842723-T-G
• rs1408272
• ENST00000481949.6:c.*2+2657A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000481949.6(SLC17A3):​c.*2+2657A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.039 in 152,154 control chromosomes in the GnomAD database, including 169 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 (169 hom., cov: 32)
• Consequence: SLC17A3 ENST00000481949.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676
• Publications: 50 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901285	XR_007059518.1	n.379+6191T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A3	ENST00000481949.6	c.*2+2657A>C		intron_variant	Intron 3 of 3	3		ENSP00000421855.1
SLC17A3	ENST00000505420.5	c.*3-916A>C		intron_variant	Intron 2 of 2	5		ENSP00000424027.1

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5926 AN: 152036 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.00950

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00518

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0390 AC: 5927 AN: 152154 Hom.: 169 Cov.: 32 AF XY: 0.0356 AC XY: 2646 AN XY: 74400

African (AFR) AF: 0.0114 AC: 473 AN: 41464

American (AMR) AF: 0.0240 AC: 367 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00950 AC: 33 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.00518 AC: 25 AN: 4822

European-Finnish (FIN) AF: 0.0348 AC: 369 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0669 AC: 4548 AN: 67990

Other (OTH) AF: 0.0322 AC: 68 AN: 2112

Alfa AF: 0.0542 Hom.: 955

Bravo AF: 0.0368

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.49
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1408272; hg19: chr6-25842951;