rs3124932
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000093.5(COL5A1):c.2430+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 1,611,542 control chromosomes in the GnomAD database, including 163,758 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.37 ( 12189 hom., cov: 33)
Exomes 𝑓: 0.45 ( 151569 hom. )
Consequence
COL5A1
NM_000093.5 intron
NM_000093.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.76
Genes affected
COL5A1 (HGNC:2209): (collagen type V alpha 1 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. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene 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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant 9-134780166-C-T is Benign according to our data. Variant chr9-134780166-C-T is described in ClinVar as [Benign]. Clinvar id is 136866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-134780166-C-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.2430+20C>T | intron_variant | ENST00000371817.8 | |||
COL5A1 | NM_001278074.1 | c.2430+20C>T | intron_variant | ||||
COL5A1 | XM_017014266.3 | c.2430+20C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.2430+20C>T | intron_variant | 1 | NM_000093.5 | P4 | |||
COL5A1 | ENST00000371820.4 | c.2430+20C>T | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.368 AC: 55888AN: 151986Hom.: 12184 Cov.: 33
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GnomAD3 exomes AF: 0.418 AC: 104628AN: 250528Hom.: 24214 AF XY: 0.426 AC XY: 57849AN XY: 135712
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GnomAD4 exome AF: 0.447 AC: 651994AN: 1459438Hom.: 151569 Cov.: 39 AF XY: 0.448 AC XY: 325358AN XY: 726128
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GnomAD4 genome ? AF: 0.368 AC: 55900AN: 152104Hom.: 12189 Cov.: 33 AF XY: 0.371 AC XY: 27607AN XY: 74340
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ClinVar
Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 02, 2012 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Ehlers-Danlos syndrome, classic type, 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Fibromuscular dysplasia, multifocal Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 15, 2017 | Variant summary: The COL5A1 c.2430+20C>T variant involves the alteration of a non-conserved intronic nucleotide. Although Mutation Taster was down at the time of this scoring, 5/5 splice prediction tools predict no significant impact on normal splicing and has no significant effect on ESE sites at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in 49278/120530 control chromosomes (11250 homozygotes) at a frequency of 0.4088443, which is approximately 327075 times the estimated maximal expected allele frequency of a pathogenic COL5A1 variant (0.0000013), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign. - |
Computational scores
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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