rs142166552
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_025243.4(SLC19A3):c.1112C>T(p.Ala371Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000354 in 1,614,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A371A) has been classified as Likely benign.
Frequency
Consequence
NM_025243.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC19A3 | NM_025243.4 | c.1112C>T | p.Ala371Val | missense_variant | 4/6 | ENST00000644224.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC19A3 | ENST00000644224.2 | c.1112C>T | p.Ala371Val | missense_variant | 4/6 | NM_025243.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000342 AC: 52AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000449 AC: 113AN: 251470Hom.: 0 AF XY: 0.000427 AC XY: 58AN XY: 135910
GnomAD4 exome AF: 0.000355 AC: 519AN: 1461876Hom.: 0 Cov.: 30 AF XY: 0.000356 AC XY: 259AN XY: 727238
GnomAD4 genome ? AF: 0.000342 AC: 52AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74430
ClinVar
Submissions by phenotype
Biotin-responsive basal ganglia disease Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Dec 10, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Jul 28, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 03, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 26, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at