2-237324819-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_004369.4(COL6A3):c.9494-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,461,092 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004369.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.9494-5C>T | splice_region_variant, intron_variant | Intron 43 of 43 | ENST00000295550.9 | NP_004360.2 | ||
COL6A3 | NM_057167.4 | c.8876-5C>T | splice_region_variant, intron_variant | Intron 42 of 42 | NP_476508.2 | |||
COL6A3 | NM_057166.5 | c.7673-5C>T | splice_region_variant, intron_variant | Intron 40 of 40 | NP_476507.3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1461092Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726784
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
- -
Bethlem myopathy 1A Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at