chr2-237324820-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_004369.4(COL6A3):c.9494-6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004369.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.9494-6G>A | splice_region_variant, intron_variant | Intron 43 of 43 | ENST00000295550.9 | NP_004360.2 | ||
COL6A3 | NM_057167.4 | c.8876-6G>A | splice_region_variant, intron_variant | Intron 42 of 42 | NP_476508.2 | |||
COL6A3 | NM_057166.5 | c.7673-6G>A | splice_region_variant, intron_variant | Intron 40 of 40 | NP_476507.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151896Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247698Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134068
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460864Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726702
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151896Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74176
ClinVar
Submissions by phenotype
Myopathy Uncertain:1
- -
Bethlem myopathy 1A Benign:1
- -
not provided Benign:1
COL6A3: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at