2-227699294-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_025243.4(SLC19A3):c.421G>A(p.Gly141Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00391 in 1,614,090 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_025243.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00423 AC: 644AN: 152102Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00423 AC: 1064AN: 251280Hom.: 3 AF XY: 0.00414 AC XY: 562AN XY: 135820
GnomAD4 exome AF: 0.00387 AC: 5664AN: 1461870Hom.: 24 Cov.: 33 AF XY: 0.00388 AC XY: 2824AN XY: 727230
GnomAD4 genome AF: 0.00423 AC: 644AN: 152220Hom.: 4 Cov.: 33 AF XY: 0.00400 AC XY: 298AN XY: 74426
ClinVar
Submissions by phenotype
Biotin-responsive basal ganglia disease Benign:5
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
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not specified Benign:4
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:3
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SLC19A3: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at