chr2-85539324-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_005911.6(MAT2A):c.37A>G(p.Ile13Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,454,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I13M) has been classified as Uncertain significance.
Frequency
Consequence
NM_005911.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAT2A | NM_005911.6 | c.37A>G | p.Ile13Val | missense_variant | 1/9 | ENST00000306434.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAT2A | ENST00000306434.8 | c.37A>G | p.Ile13Val | missense_variant | 1/9 | 1 | NM_005911.6 | P1 | |
MAT2A | ENST00000465151.5 | n.157A>G | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
MAT2A | ENST00000469221.5 | n.157A>G | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 243084Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132122
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1454742Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3AN XY: 723814
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 19, 2023 | This variant is present in population databases (rs760251833, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with MAT2A-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 13 of the MAT2A protein (p.Ile13Val). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at