rs117195882
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000030.3(AGXT):c.557C>T(p.Ala186Val) variant causes a missense change. The variant allele was found at a frequency of 0.00453 in 1,613,864 control chromosomes in the GnomAD database, including 207 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000030.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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AGXT | ENST00000307503.4 | c.557C>T | p.Ala186Val | missense_variant | Exon 5 of 11 | 1 | NM_000030.3 | ENSP00000302620.3 | ||
AGXT | ENST00000472436.1 | n.577C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 2 | |||||
AGXT | ENST00000476698.1 | n.294C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00410 AC: 624AN: 152162Hom.: 22 Cov.: 32
GnomAD3 exomes AF: 0.0113 AC: 2811AN: 249728Hom.: 92 AF XY: 0.0119 AC XY: 1613AN XY: 135090
GnomAD4 exome AF: 0.00457 AC: 6684AN: 1461584Hom.: 185 Cov.: 31 AF XY: 0.00527 AC XY: 3835AN XY: 727114
GnomAD4 genome AF: 0.00408 AC: 622AN: 152280Hom.: 22 Cov.: 32 AF XY: 0.00496 AC XY: 369AN XY: 74440
ClinVar
Submissions by phenotype
Primary hyperoxaluria, type I Benign:4
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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Found in cis with c.590G>A in 2 unrelated individuals. ACMG:PM2 PP3 BP2 BP5 -
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not provided Benign:3
This variant is associated with the following publications: (PMID: 30341509, 33457257) -
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at