rs200245740
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001848.3(COL6A1):c.1674+46_1674+47dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00394 in 1,548,928 control chromosomes in the GnomAD database, including 71 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 34 hom., cov: 34)
Exomes 𝑓: 0.0030 ( 37 hom. )
Consequence
COL6A1
NM_001848.3 intron
NM_001848.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.72
Genes affected
COL6A1 (HGNC:2211): (collagen type VI alpha 1 chain) The collagens are a superfamily of proteins that play a role in maintaining the integrity of various tissues. Collagens are extracellular matrix proteins and have a triple-helical domain as their common structural element. Collagen VI is a major structural component of microfibrils. The basic structural unit of collagen VI is a heterotrimer of the alpha1(VI), alpha2(VI), and alpha3(VI) chains. The alpha2(VI) and alpha3(VI) chains are encoded by the COL6A2 and COL6A3 genes, respectively. The protein encoded by this gene is the alpha 1 subunit of type VI collagen (alpha1(VI) chain). Mutations in the genes that code for the collagen VI subunits result in the autosomal dominant disorder, Bethlem myopathy. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 21-45999004-C-CCA is Benign according to our data. Variant chr21-45999004-C-CCA is described in ClinVar as [Benign]. Clinvar id is 258292.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1954/152280) while in subpopulation AFR AF= 0.0378 (1571/41556). AF 95% confidence interval is 0.0362. There are 34 homozygotes in gnomad4. There are 957 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 34 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.1674+46_1674+47dup | intron_variant | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.1674+46_1674+47dup | intron_variant | 1 | NM_001848.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0127 AC: 1936AN: 152162Hom.: 30 Cov.: 34
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GnomAD3 exomes AF: 0.00446 AC: 692AN: 155114Hom.: 7 AF XY: 0.00371 AC XY: 304AN XY: 81898
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GnomAD4 exome AF: 0.00297 AC: 4147AN: 1396648Hom.: 37 Cov.: 32 AF XY: 0.00277 AC XY: 1907AN XY: 688724
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GnomAD4 genome ? AF: 0.0128 AC: 1954AN: 152280Hom.: 34 Cov.: 34 AF XY: 0.0129 AC XY: 957AN XY: 74470
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at