rs146207015
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005911.6(MAT2A):c.666A>G(p.Leu222=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000165 in 1,614,026 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L222L) has been classified as Likely benign.
Frequency
Consequence
NM_005911.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAT2A | NM_005911.6 | c.666A>G | p.Leu222= | synonymous_variant | 6/9 | ENST00000306434.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAT2A | ENST00000306434.8 | c.666A>G | p.Leu222= | synonymous_variant | 6/9 | 1 | NM_005911.6 | P1 | |
MAT2A | ENST00000409017.1 | c.477A>G | p.Leu159= | synonymous_variant | 6/8 | 1 | |||
MAT2A | ENST00000481412.5 | n.644A>G | non_coding_transcript_exon_variant | 6/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251440Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135888
GnomAD4 exome AF: 0.000171 AC: 250AN: 1461810Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 127AN XY: 727204
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74366
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 26, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 25, 2020 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at