chr12-6935964-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001940.4(ATN1):c.697A>G(p.Met233Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000323 in 1,590,444 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_001940.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATN1 | NM_001940.4 | c.697A>G | p.Met233Val | missense_variant | 5/10 | ENST00000396684.3 | |
ATN1 | NM_001007026.2 | c.697A>G | p.Met233Val | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.697A>G | p.Met233Val | missense_variant | 5/10 | 1 | NM_001940.4 | P1 | |
ATN1 | ENST00000356654.8 | c.697A>G | p.Met233Val | missense_variant | 5/10 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000382 AC: 58AN: 151770Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000188 AC: 43AN: 228488Hom.: 0 AF XY: 0.000146 AC XY: 18AN XY: 123708
GnomAD4 exome AF: 0.000317 AC: 456AN: 1438552Hom.: 0 Cov.: 37 AF XY: 0.000300 AC XY: 214AN XY: 713674
GnomAD4 genome ? AF: 0.000382 AC: 58AN: 151892Hom.: 0 Cov.: 31 AF XY: 0.000323 AC XY: 24AN XY: 74240
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | 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