rs5852593
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001278298.2(COL6A5):c.668-615dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,010 control chromosomes in the GnomAD database, including 7,152 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.29 ( 7152 hom., cov: 21)
Consequence
COL6A5
NM_001278298.2 intron
NM_001278298.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0280
Genes affected
COL6A5 (HGNC:26674): (collagen type VI alpha 5 chain) This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A5 | NM_001278298.2 | c.668-615dup | intron_variant | ENST00000373157.9 | |||
COL6A5 | NM_153264.7 | c.668-615dup | intron_variant | ||||
COL6A5 | NR_022012.3 | n.1006-615dup | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A5 | ENST00000373157.9 | c.668-615dup | intron_variant | 2 | NM_001278298.2 | P2 | |||
COL6A5 | ENST00000312481.11 | c.668-615dup | intron_variant, NMD_transcript_variant | 1 | |||||
COL6A5 | ENST00000512836.6 | c.668-615dup | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.286 AC: 43453AN: 151894Hom.: 7121 Cov.: 21
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.286 AC: 43539AN: 152010Hom.: 7152 Cov.: 21 AF XY: 0.287 AC XY: 21321AN XY: 74324
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ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at