chr2-85754527-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032827.7(ATOH8):c.338C>T(p.Ala113Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000559 in 1,431,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032827.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATOH8 | ENST00000306279.4 | c.338C>T | p.Ala113Val | missense_variant | Exon 1 of 3 | 1 | NM_032827.7 | ENSP00000304676.3 | ||
ATOH8 | ENST00000469442.5 | n.519+2665C>T | intron_variant | Intron 1 of 2 | 2 | |||||
ATOH8 | ENST00000463422.5 | n.-120C>T | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000902 AC: 3AN: 33256Hom.: 0 AF XY: 0.0000532 AC XY: 1AN XY: 18804
GnomAD4 exome AF: 0.00000469 AC: 6AN: 1278780Hom.: 0 Cov.: 30 AF XY: 0.00000320 AC XY: 2AN XY: 625080
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.338C>T (p.A113V) alteration is located in exon 1 (coding exon 1) of the ATOH8 gene. This alteration results from a C to T substitution at nucleotide position 338, causing the alanine (A) at amino acid position 113 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at