9-134642173-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_000093.5(COL5A1):c.-15C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,251,258 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 3 hom. )
Consequence
COL5A1
NM_000093.5 5_prime_UTR
NM_000093.5 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 2.75
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=-0.36).
BP6
?
Variant 9-134642173-C-A is Benign according to our data. Variant chr9-134642173-C-A is described in ClinVar as [Benign]. Clinvar id is 136923.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd at 169 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.-15C>A | 5_prime_UTR_variant | 1/66 | ENST00000371817.8 | ||
COL5A1 | NM_001278074.1 | c.-15C>A | 5_prime_UTR_variant | 1/66 | |||
COL5A1 | XM_017014266.3 | c.-15C>A | 5_prime_UTR_variant | 1/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.-15C>A | 5_prime_UTR_variant | 1/66 | 1 | NM_000093.5 | P4 | ||
COL5A1 | ENST00000371820.4 | c.-15C>A | 5_prime_UTR_variant | 1/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00112 AC: 169AN: 151480Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00119 AC: 11AN: 9234Hom.: 0 AF XY: 0.00100 AC XY: 6AN XY: 5990
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GnomAD4 exome AF: 0.00114 AC: 1249AN: 1099670Hom.: 3 Cov.: 31 AF XY: 0.00112 AC XY: 588AN XY: 527084
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GnomAD4 genome ? AF: 0.00111 AC: 169AN: 151588Hom.: 0 Cov.: 32 AF XY: 0.00115 AC XY: 85AN XY: 74072
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Oct 29, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 07, 2013 | 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. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at