NM_004369.4:c.*665G>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004369.4(COL6A3):c.*665G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 149,242 control chromosomes in the GnomAD database, including 32,004 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004369.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.*665G>T | 3_prime_UTR_variant | Exon 44 of 44 | ENST00000295550.9 | NP_004360.2 | ||
COL6A3 | NM_057167.4 | c.*665G>T | 3_prime_UTR_variant | Exon 43 of 43 | NP_476508.2 | |||
COL6A3 | NM_057166.5 | c.*665G>T | 3_prime_UTR_variant | Exon 41 of 41 | NP_476507.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.654 AC: 97230AN: 148732Hom.: 31915 Cov.: 30
GnomAD4 exome AF: 0.574 AC: 240AN: 418Hom.: 58 Cov.: 0 AF XY: 0.571 AC XY: 144AN XY: 252
GnomAD4 genome AF: 0.654 AC: 97314AN: 148824Hom.: 31946 Cov.: 30 AF XY: 0.652 AC XY: 47274AN XY: 72498
ClinVar
Submissions by phenotype
Collagen 6-related myopathy Benign: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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at