rs201278545
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_144670.6(A2ML1):c.3297G>A(p.Ala1099=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,614,086 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. A1099A) has been classified as Likely benign.
Frequency
Consequence
NM_144670.6 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 |
---|---|---|---|---|---|---|---|
A2ML1 | NM_144670.6 | c.3297G>A | p.Ala1099= | synonymous_variant | 27/36 | ENST00000299698.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
A2ML1 | ENST00000299698.12 | c.3297G>A | p.Ala1099= | synonymous_variant | 27/36 | 1 | NM_144670.6 | P1 | |
ENST00000631830.1 | n.322-2637C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
A2ML1 | ENST00000541459.5 | c.1947G>A | p.Ala649= | synonymous_variant | 16/25 | 2 | |||
A2ML1 | ENST00000539547.5 | c.1824G>A | p.Ala608= | synonymous_variant | 16/25 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000962 AC: 24AN: 249572Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135396
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 727246
GnomAD4 genome ? AF: 0.0000986 AC: 15AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74408
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at