chr6-25869143-G-C

Variant names:

• chr6-25869143-G-C
• rs548987
• NM_001098486.2:c.-33-723C>G

Variant summary

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

The NM_001098486.2(SLC17A3):​c.-33-723C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,888 control chromosomes in the GnomAD database, including 4,223 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 (4223 hom., cov: 32)
• Consequence: SLC17A3 NM_001098486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 45 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098486.2. 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
	SLC17A3	NM_001098486.2	MANE Select	c.-33-723C>G		intron	N/A	NP_001091956.1
	SLC17A3	NM_006632.4		c.-33-723C>G		intron	N/A	NP_006623.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A3	ENST00000397060.8	TSL:2 MANE Select	c.-33-723C>G		intron	N/A	ENSP00000380250.4
	SLC17A3	ENST00000361703.10	TSL:1	c.-33-723C>G		intron	N/A	ENSP00000355307.6
	SLC17A3	ENST00000360657.7	TSL:2	c.-33-723C>G		intron	N/A	ENSP00000353873.3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29727 AN: 151770 Hom.: 4216 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.196 AC: 29750 AN: 151888 Hom.: 4223 Cov.: 32 AF XY: 0.191 AC XY: 14203 AN XY: 74234

African (AFR) AF: 0.400 AC: 16548 AN: 41414

American (AMR) AF: 0.137 AC: 2084 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3468

East Asian (EAS) AF: 0.130 AC: 670 AN: 5138

South Asian (SAS) AF: 0.0631 AC: 304 AN: 4820

European-Finnish (FIN) AF: 0.0847 AC: 898 AN: 10596

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8372 AN: 67880

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.169 Hom.: 381

Bravo AF: 0.213

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.37
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs548987; hg19: chr6-25869371;