chr21-45981859-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001848.3(COL6A1):c.9G>A(p.Ala3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,588,768 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 (★). Synonymous variant affecting the same amino acid position (i.e. A3A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001848.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.9G>A | p.Ala3= | synonymous_variant | 1/35 | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.9G>A | p.Ala3= | synonymous_variant | 1/35 | 1 | NM_001848.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150562Hom.: 0 Cov.: 29
GnomAD4 exome AF: 0.0000111 AC: 16AN: 1438206Hom.: 0 Cov.: 33 AF XY: 0.00000981 AC XY: 7AN XY: 713738
GnomAD4 genome AF: 0.00000664 AC: 1AN: 150562Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 73428
ClinVar
Submissions by phenotype
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at