rs547487220
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000036.3(AMPD1):c.323C>T(p.Thr108Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,614,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000036.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMPD1 | NM_000036.3 | c.323C>T | p.Thr108Ile | missense_variant | 4/16 | ENST00000520113.7 | |
AMPD1 | NM_001172626.2 | c.311C>T | p.Thr104Ile | missense_variant | 3/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMPD1 | ENST00000520113.7 | c.323C>T | p.Thr108Ile | missense_variant | 4/16 | 1 | NM_000036.3 | P4 | |
AMPD1 | ENST00000369538.4 | c.311C>T | p.Thr104Ile | missense_variant | 3/15 | 2 | A1 | ||
AMPD1 | ENST00000485564.3 | n.197C>T | non_coding_transcript_exon_variant | 1/3 | 5 | ||||
AMPD1 | ENST00000637080.1 | c.326C>T | p.Thr109Ile | missense_variant, NMD_transcript_variant | 3/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000255 AC: 64AN: 251468Hom.: 0 AF XY: 0.000272 AC XY: 37AN XY: 135906
GnomAD4 exome AF: 0.000107 AC: 156AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.000149 AC XY: 108AN XY: 727232
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74464
ClinVar
Submissions by phenotype
Muscle AMP deaminase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at