1-234373707-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001012985.2(COA6):c.-12C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,284 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_001012985.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COA6 | NM_001206641.3 | c.212+29C>T | intron_variant | Intron 1 of 2 | ENST00000366615.10 | NP_001193570.2 | ||
COA6 | NM_001012985.2 | c.-12C>T | 5_prime_UTR_variant | Exon 1 of 3 | NP_001013003.1 | |||
COA6 | NM_001301733.1 | c.-539C>T | 5_prime_UTR_variant | Exon 1 of 2 | NP_001288662.1 | |||
COA6-AS1 | NR_125961.1 | n.-114G>A | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250228Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135284
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461070Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 726736
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at