12-70310991-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_014515.7(CNOT2):c.145A>G(p.Met49Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000313 in 1,599,708 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 (★★).
Frequency
Consequence
NM_014515.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNOT2 | NM_014515.7 | c.145A>G | p.Met49Val | missense_variant | Exon 3 of 16 | ENST00000229195.8 | NP_055330.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249716Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135012
GnomAD4 exome AF: 0.0000304 AC: 44AN: 1447602Hom.: 0 Cov.: 26 AF XY: 0.0000374 AC XY: 27AN XY: 720988
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74312
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
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
CNOT2: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at