19-3885803-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_033064.5(ATCAY):c.36C>T(p.Asn12Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000646 in 1,552,240 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_033064.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATCAY | NM_033064.5 | c.36C>T | p.Asn12Asn | synonymous_variant | Exon 2 of 13 | ENST00000450849.7 | NP_149053.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000585 AC: 89AN: 152112Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000565 AC: 89AN: 157478Hom.: 0 AF XY: 0.000541 AC XY: 45AN XY: 83254
GnomAD4 exome AF: 0.000653 AC: 914AN: 1400010Hom.: 3 Cov.: 31 AF XY: 0.000599 AC XY: 414AN XY: 690590
GnomAD4 genome AF: 0.000585 AC: 89AN: 152230Hom.: 0 Cov.: 31 AF XY: 0.000672 AC XY: 50AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:2
- -
ATCAY: BP4, BP7 -
Cayman type cerebellar ataxia Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at