rs9461219

chr6-25836699-C-Gchr6-25836699-C-T

Variant summary

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

The XR_007059518.1(LOC124901285):n.379+167C>G 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 0.0723 in 152,040 control chromosomes in the GnomAD database, including 436 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 0.072 (436 hom., cov: 31)
• Consequence: LOC124901285 XR_007059518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

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=-0.98).
• 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
LOC124901285	XR_007059518.1	n.379+167C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A3	ENST00000481949.6	c.*3-3336G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0724 AC: 10997 AN: 151922 Hom.: 437 Cov.: 31

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0723 AC: 10993 AN: 152040 Hom.: 436 Cov.: 31 AF XY: 0.0680 AC XY: 5055 AN XY: 74324

Gnomad4 AFR AF: 0.0837

Gnomad4 AMR AF: 0.0523

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0151

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0393

Gnomad4 NFE AF: 0.0868

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0313 Hom.: 24

Bravo AF: 0.0758

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.75
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9461219; hg19: chr6-25836927;