rs942379
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001098486.2(SLC17A3):āc.1344T>Cā(p.Ser448=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 1,604,642 control chromosomes in the GnomAD database, including 269,051 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: š 0.65 ( 33604 hom., cov: 31)
Exomes š: 0.56 ( 235447 hom. )
Consequence
SLC17A3
NM_001098486.2 synonymous
NM_001098486.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.632
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP7
Synonymous conserved (PhyloP=-0.632 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC17A3 | NM_001098486.2 | c.1344T>C | p.Ser448= | synonymous_variant | 11/13 | ENST00000397060.8 | |
LOC124901285 | XR_007059518.1 | n.380-10254A>G | intron_variant, non_coding_transcript_variant | ||||
SLC17A3 | NM_006632.4 | c.1110T>C | p.Ser370= | synonymous_variant | 10/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC17A3 | ENST00000397060.8 | c.1344T>C | p.Ser448= | synonymous_variant | 11/13 | 2 | NM_001098486.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.647 AC: 98153AN: 151820Hom.: 33543 Cov.: 31
GnomAD3 genomes
AF:
AC:
98153
AN:
151820
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.600 AC: 150403AN: 250766Hom.: 47299 AF XY: 0.583 AC XY: 79004AN XY: 135540
GnomAD3 exomes
AF:
AC:
150403
AN:
250766
Hom.:
AF XY:
AC XY:
79004
AN XY:
135540
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.563 AC: 817517AN: 1452704Hom.: 235447 Cov.: 31 AF XY: 0.558 AC XY: 403731AN XY: 723276
GnomAD4 exome
AF:
AC:
817517
AN:
1452704
Hom.:
Cov.:
31
AF XY:
AC XY:
403731
AN XY:
723276
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.647 AC: 98277AN: 151938Hom.: 33604 Cov.: 31 AF XY: 0.647 AC XY: 47999AN XY: 74242
GnomAD4 genome
AF:
AC:
98277
AN:
151938
Hom.:
Cov.:
31
AF XY:
AC XY:
47999
AN XY:
74242
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2307
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at