ENST00000481949.6:c.*3-3336G>C

Variant names:

• chr6-25836699-C-G
• rs9461219
• ENST00000481949.6:c.*3-3336G>C

Variant summary

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

The ENST00000481949.6(SLC17A3):​c.*3-3336G>C variant causes a intron 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: SLC17A3 ENST00000481949.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0849 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000481949.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A3	ENST00000481949.6	TSL:3	c.*3-3336G>C		intron	N/A	ENSP00000421855.1

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

African (AFR) AF: 0.0837 AC: 3470 AN: 41456

American (AMR) AF: 0.0523 AC: 799 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3470

East Asian (EAS) AF: 0.0151 AC: 78 AN: 5170

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4822

European-Finnish (FIN) AF: 0.0393 AC: 415 AN: 10562

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5898 AN: 67962

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.75
DANN	Benign	0.40
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs9461219; hg19: chr6-25836927;