rs7420331
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000393.5(COL5A2):c.456+1674T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,026 control chromosomes in the GnomAD database, including 1,365 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 0.13 ( 1365 hom., cov: 30)
Consequence
COL5A2
NM_000393.5 intron
NM_000393.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.41
Genes affected
COL5A2 (HGNC:2210): (collagen type V alpha 2 chain) This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. [provided by RefSeq, Jul 2008]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.456+1674T>C | intron_variant | ENST00000374866.9 | |||
COL5A2 | XM_011510573.4 | c.318+1674T>C | intron_variant | ||||
COL5A2 | XM_047443251.1 | c.318+1674T>C | intron_variant | ||||
COL5A2 | XM_047443252.1 | c.318+1674T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.456+1674T>C | intron_variant | 1 | NM_000393.5 | P1 | |||
ENST00000419029.1 | n.75-233A>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
COL5A2 | ENST00000618828.1 | c.-175+1674T>C | intron_variant | 5 | |||||
COL5A2 | ENST00000649966.1 | c.318+1674T>C | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.133 AC: 20188AN: 151908Hom.: 1368 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.133 AC: 20181AN: 152026Hom.: 1365 Cov.: 30 AF XY: 0.134 AC XY: 9959AN XY: 74346
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477
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3478
ClinVar
Not reported inComputational scores
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Name
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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