rs1542829
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001278298.2(COL6A5):c.4888-242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0823 in 152,042 control chromosomes in the GnomAD database, including 614 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.082 ( 614 hom., cov: 31)
Consequence
COL6A5
NM_001278298.2 intron
NM_001278298.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.296
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A5 | NM_001278298.2 | c.4888-242G>A | intron_variant | ENST00000373157.9 | |||
COL6A5 | NM_153264.7 | c.4888-242G>A | intron_variant | ||||
COL6A5 | NR_022012.3 | n.5226-242G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A5 | ENST00000373157.9 | c.4888-242G>A | intron_variant | 2 | NM_001278298.2 | P2 | |||
COL6A5 | ENST00000312481.11 | c.4888-242G>A | intron_variant, NMD_transcript_variant | 1 | |||||
COL6A5 | ENST00000512836.6 | c.4888-242G>A | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0822 AC: 12489AN: 151924Hom.: 613 Cov.: 31
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0823 AC: 12511AN: 152042Hom.: 614 Cov.: 31 AF XY: 0.0839 AC XY: 6235AN XY: 74328
GnomAD4 genome
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74328
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587
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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