chr2-240507580-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001282771.3(ANKMY1):c.2506A>G(p.Met836Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000485 in 1,609,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001282771.3 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 |
---|---|---|---|---|---|---|---|
ANKMY1 | NM_001282771.3 | c.2506A>G | p.Met836Val | missense_variant | 13/18 | ENST00000401804.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKMY1 | ENST00000401804.6 | c.2506A>G | p.Met836Val | missense_variant | 13/18 | 1 | NM_001282771.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 34AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000483 AC: 12AN: 248196Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134140
GnomAD4 exome AF: 0.0000295 AC: 43AN: 1457250Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 724662
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | 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