chr21-45981850-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001848.3(COL6A1):c.-1C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000259 in 1,582,836 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 Uncertain significance (★★).
Frequency
Consequence
NM_001848.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 35 | ENST00000361866.8 | NP_001839.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150514Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000154 AC: 3AN: 194752Hom.: 0 AF XY: 0.0000188 AC XY: 2AN XY: 106608
GnomAD4 exome AF: 0.0000279 AC: 40AN: 1432322Hom.: 0 Cov.: 32 AF XY: 0.0000253 AC XY: 18AN XY: 710398
GnomAD4 genome AF: 0.00000664 AC: 1AN: 150514Hom.: 0 Cov.: 29 AF XY: 0.0000136 AC XY: 1AN XY: 73424
ClinVar
Submissions by phenotype
not provided Uncertain:3
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Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 30564623) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at