rs548987

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.242
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC17A3NM_001098486.2 linkuse as main transcriptc.-33-723C>G intron_variant ENST00000397060.8
SLC17A3NM_006632.4 linkuse as main transcriptc.-33-723C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC17A3ENST00000397060.8 linkuse as main transcriptc.-33-723C>G intron_variant 2 NM_001098486.2 P1O00476-2

Frequencies

GnomAD3 genomes
AF:
0.196
AC:
29727
AN:
151770
Hom.:
4216
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.400
Gnomad4 AMR
AF:
0.137
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.130
Gnomad4 SAS
AF:
0.0631
Gnomad4 FIN
AF:
0.0847
Gnomad4 NFE
AF:
0.123
Gnomad4 OTH
AF:
0.185
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.69
DANN
Benign
0.37

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs548987; hg19: chr6-25869371; API