rs55748801
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000093.5(COL5A1):c.*190G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00898 in 684,656 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0057 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0099 ( 61 hom. )
Consequence
COL5A1
NM_000093.5 3_prime_UTR
NM_000093.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.02
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 9-134842493-G-A is Benign according to our data. Variant chr9-134842493-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 365744.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00575 (875/152268) while in subpopulation SAS AF= 0.027 (130/4818). AF 95% confidence interval is 0.0232. There are 9 homozygotes in gnomad4. There are 429 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 869 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.*190G>A | 3_prime_UTR_variant | 66/66 | ENST00000371817.8 | ||
LOC101448202 | NR_103451.2 | n.71-22284C>T | intron_variant, non_coding_transcript_variant | ||||
COL5A1 | NM_001278074.1 | c.*190G>A | 3_prime_UTR_variant | 66/66 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.*190G>A | 3_prime_UTR_variant | 66/66 | 1 | NM_000093.5 | P4 | ||
COL5A1 | ENST00000371820.4 | c.*190G>A | 3_prime_UTR_variant | 66/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00571 AC: 869AN: 152150Hom.: 9 Cov.: 32
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GnomAD4 exome AF: 0.00991 AC: 5274AN: 532388Hom.: 61 Cov.: 6 AF XY: 0.0113 AC XY: 3157AN XY: 279638
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GnomAD4 genome ? AF: 0.00575 AC: 875AN: 152268Hom.: 9 Cov.: 32 AF XY: 0.00576 AC XY: 429AN XY: 74444
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
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 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at