rs780668
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018344.6(SLC29A3):c.473C>T(p.Ser158Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.701 in 1,613,958 control chromosomes in the GnomAD database, including 409,244 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign,drug response (★★). Synonymous variant affecting the same amino acid position (i.e. S158S) has been classified as Likely benign.
Frequency
Consequence
NM_018344.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC29A3 | NM_018344.6 | c.473C>T | p.Ser158Phe | missense_variant | 4/6 | ENST00000373189.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC29A3 | ENST00000373189.6 | c.473C>T | p.Ser158Phe | missense_variant | 4/6 | 1 | NM_018344.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.613 AC: 93188AN: 151976Hom.: 31124 Cov.: 32
GnomAD3 exomes AF: 0.639 AC: 160758AN: 251472Hom.: 54270 AF XY: 0.650 AC XY: 88296AN XY: 135908
GnomAD4 exome AF: 0.711 AC: 1038771AN: 1461864Hom.: 378130 Cov.: 63 AF XY: 0.708 AC XY: 514870AN XY: 727236
GnomAD4 genome ? AF: 0.613 AC: 93189AN: 152094Hom.: 31114 Cov.: 32 AF XY: 0.610 AC XY: 45321AN XY: 74356
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 86% of patients studied by a panel of primary immunodeficiencies. Number of patients: 83. Only high quality variants are reported. - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 11, 2018 | - - |
H syndrome Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | This variant is associated with the following publications: (PMID: 28842327) - |
Gemcitabine response Other:1
drug response, criteria provided, single submitter | research | Bioinformatics Institute, Agency for Science, Technology and Research | Jan 01, 2017 | - correlated with patient outcome with gemcitabine-based chemotherpy |
Acanthosis nigricans Other:1
association, no assertion criteria provided | research | Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic | - | Mutations in this gene can predispose to acanthosis nigricans in patients with insulin dependent diabetes. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at