chr1-114677465-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP3BP4_Strong
The NM_000036.3(AMPD1):c.1274G>A(p.Arg425His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,613,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R425C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000036.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000410 AC: 62AN: 151150Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.000875 AC: 220AN: 251428Hom.: 3 AF XY: 0.000839 AC XY: 114AN XY: 135892
GnomAD4 exome AF: 0.000242 AC: 354AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.000252 AC XY: 183AN XY: 727246
GnomAD4 genome AF: 0.000410 AC: 62AN: 151266Hom.: 0 Cov.: 28 AF XY: 0.000528 AC XY: 39AN XY: 73846
ClinVar
Submissions by phenotype
Muscle AMP deaminase deficiency Pathogenic:2Uncertain:2Benign:1
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not specified Uncertain:1
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not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at