chr21-45994228-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001848.3(COL6A1):āc.1397C>Gā(p.Pro466Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000412 in 1,456,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P466L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001848.3 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.1397C>G | p.Pro466Arg | missense_variant, splice_region_variant | 20/35 | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.1397C>G | p.Pro466Arg | missense_variant, splice_region_variant | 20/35 | 1 | NM_001848.3 | P1 | |
COL6A1 | ENST00000683550.1 | n.172C>G | splice_region_variant, non_coding_transcript_exon_variant | 1/5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000252 AC: 6AN: 237828Hom.: 0 AF XY: 0.0000310 AC XY: 4AN XY: 128938
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1456786Hom.: 0 Cov.: 32 AF XY: 0.00000552 AC XY: 4AN XY: 724096
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at