rs1324087

Variant names:

• chr6-25841180-G-A
• rs1324087
• ENST00000481949.6:c.*2+4200C>T

Variant summary

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

The ENST00000481949.6(SLC17A3):​c.*2+4200C>T variant causes a intron 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: SLC17A3 ENST00000481949.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 19 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=-0.86).
• 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 rank	MANE	Protein	UniProt
LOC124901285	XR_007059518.1	n.379+4648G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A3	ENST00000481949.6	c.*2+4200C>T		intron_variant	Intron 3 of 3	3		ENSP00000421855.1
SLC17A3	ENST00000505420.5	c.*630C>T		downstream_gene_variant		5		ENSP00000424027.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.255 AC: 10570 AN: 41488

American (AMR) AF: 0.109 AC: 1667 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3470

East Asian (EAS) AF: 0.118 AC: 612 AN: 5186

South Asian (SAS) AF: 0.0588 AC: 284 AN: 4828

European-Finnish (FIN) AF: 0.0845 AC: 896 AN: 10608

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8044 AN: 68002

Other (OTH) AF: 0.148 AC: 312 AN: 2114

Alfa AF: 0.135 Hom.: 3670

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1324087; hg19: chr6-25841408;