chr2-3499065-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018269.4(ADI1):c.438G>A(p.Met146Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018269.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADI1 | ENST00000327435.11 | c.438G>A | p.Met146Ile | missense_variant | Exon 4 of 4 | 1 | NM_018269.4 | ENSP00000333666.3 | ||
ADI1 | ENST00000382093.5 | c.420G>A | p.Met140Ile | missense_variant | Exon 4 of 4 | 2 | ENSP00000371525.5 | |||
ADI1 | ENST00000415131.1 | c.249G>A | p.Met83Ile | missense_variant | Exon 2 of 2 | 3 | ENSP00000410178.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251416Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135884
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461622Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727064
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.438G>A (p.M146I) alteration is located in exon 4 (coding exon 4) of the ADI1 gene. This alteration results from a G to A substitution at nucleotide position 438, causing the methionine (M) at amino acid position 146 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at