chr12-6935973-A-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001940.4(ATN1):c.706A>C(p.Lys236Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00586 in 1,590,362 control chromosomes in the GnomAD database, including 42 homozygotes. 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 -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATN1 | NM_001940.4 | c.706A>C | p.Lys236Gln | missense_variant | 5/10 | ENST00000396684.3 | |
ATN1 | NM_001007026.2 | c.706A>C | p.Lys236Gln | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.706A>C | p.Lys236Gln | missense_variant | 5/10 | 1 | NM_001940.4 | P1 | |
ATN1 | ENST00000356654.8 | c.706A>C | p.Lys236Gln | missense_variant | 5/10 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00384 AC: 584AN: 152002Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00354 AC: 798AN: 225474Hom.: 6 AF XY: 0.00352 AC XY: 430AN XY: 122082
GnomAD4 exome AF: 0.00608 AC: 8742AN: 1438242Hom.: 40 Cov.: 38 AF XY: 0.00585 AC XY: 4178AN XY: 713588
GnomAD4 genome ? AF: 0.00384 AC: 584AN: 152120Hom.: 2 Cov.: 31 AF XY: 0.00359 AC XY: 267AN XY: 74356
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | ATN1: BS2 - |
Congenital hypotonia, epilepsy, developmental delay, and digital anomalies Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at