ENST00000861066.1:c.-34+1355T>A

Variant names:

• chr6-25880679-A-T
• rs12192635
• ENST00000861066.1:c.-34+1355T>A

Variant summary

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

The ENST00000861066.1(SLC17A3):​c.-34+1355T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,096 control chromosomes in the GnomAD database, including 3,564 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 0.20 (3564 hom., cov: 32)
• Consequence: SLC17A3 ENST00000861066.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 4 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000861066.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A3	ENST00000861066.1		c.-34+1355T>A		intron	N/A	ENSP00000531125.1
	SLC17A3	ENST00000861072.1		c.-34+1355T>A		intron	N/A	ENSP00000531131.1
	SLC17A3	ENST00000360657.7	TSL:2	c.-34+1355T>A		intron	N/A	ENSP00000353873.3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30873 AN: 151978 Hom.: 3563 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.203 AC: 30880 AN: 152096 Hom.: 3564 Cov.: 32 AF XY: 0.206 AC XY: 15301 AN XY: 74368

African (AFR) AF: 0.122 AC: 5057 AN: 41496

American (AMR) AF: 0.182 AC: 2777 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3466

East Asian (EAS) AF: 0.164 AC: 849 AN: 5168

South Asian (SAS) AF: 0.139 AC: 671 AN: 4824

European-Finnish (FIN) AF: 0.364 AC: 3845 AN: 10568

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16347 AN: 67974

Other (OTH) AF: 0.189 AC: 398 AN: 2110

Alfa AF: 0.225 Hom.: 507

Bravo AF: 0.186

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.59
PhyloP100		0.083
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12192635; hg19: chr6-25880907;