rs11186
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000393.5(COL5A2):c.*1402T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,420 control chromosomes in the GnomAD database, including 720 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.095 ( 720 hom., cov: 32)
Exomes 𝑓: 0.087 ( 0 hom. )
Consequence
COL5A2
NM_000393.5 3_prime_UTR
NM_000393.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00400
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 2-189032668-A-C is Benign according to our data. Variant chr2-189032668-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 333106.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.*1402T>G | 3_prime_UTR_variant | 54/54 | ENST00000374866.9 | ||
COL5A2 | XM_011510573.4 | c.*1402T>G | 3_prime_UTR_variant | 57/57 | |||
COL5A2 | XM_047443251.1 | c.*1402T>G | 3_prime_UTR_variant | 59/59 | |||
COL5A2 | XM_047443252.1 | c.*1402T>G | 3_prime_UTR_variant | 58/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.*1402T>G | 3_prime_UTR_variant | 54/54 | 1 | NM_000393.5 | P1 | ||
COL5A2 | ENST00000618828.1 | c.*1402T>G | 3_prime_UTR_variant | 47/47 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0955 AC: 14522AN: 152046Hom.: 720 Cov.: 32
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GnomAD4 exome AF: 0.0866 AC: 22AN: 254Hom.: 0 Cov.: 0 AF XY: 0.0671 AC XY: 11AN XY: 164
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GnomAD4 genome ? AF: 0.0955 AC: 14525AN: 152166Hom.: 720 Cov.: 32 AF XY: 0.0968 AC XY: 7203AN XY: 74402
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Ehlers-Danlos syndrome type 7A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Ehlers-Danlos syndrome, classic type, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
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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