rs1324087

chr6-25841180-G-A

Variant summary

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

The XR_007059518.1(LOC124901285):n.379+4648G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,192 control chromosomes in the GnomAD database, including 2,065 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 0.15 (2065 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC124901285 XR_007059518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55

Genes affected

LOC124901285 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901285	XR_007059518.1	n.379+4648G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A3	ENST00000481949.6	c.*2+4200C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22822 AN: 152074 Hom.: 2063 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.150

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.150 AC: 22835 AN: 152192 Hom.: 2065 Cov.: 32 AF XY: 0.147 AC XY: 10907 AN XY: 74402

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0588

Gnomad4 FIN AF: 0.0845

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.148

Alfa AF: 0.124 Hom.: 1754

Bravo AF: 0.159

Asia WGS AF: 0.0800 AC: 277 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	5.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324087; hg19: chr6-25841408;