rs878967711
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_000393.5(COL5A2):c.2086-13_2086-12del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 1,055,026 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00089 ( 0 hom., cov: 0)
Exomes 𝑓: 0.039 ( 0 hom. )
Consequence
COL5A2
NM_000393.5 splice_polypyrimidine_tract, intron
NM_000393.5 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.50
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 -16 ACMG points.
BP6
?
Variant 2-189058904-ATT-A is Benign according to our data. Variant chr2-189058904-ATT-A is described in ClinVar as [Benign]. Clinvar id is 517024.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-189058904-ATT-A is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.039 (35320/905650) while in subpopulation NFE AF= 0.0416 (27760/667576). AF 95% confidence interval is 0.0412. There are 0 homozygotes in gnomad4_exome. There are 17290 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 133 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.2086-13_2086-12del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000374866.9 | |||
COL5A2 | XM_011510573.4 | c.1948-13_1948-12del | splice_polypyrimidine_tract_variant, intron_variant | ||||
COL5A2 | XM_047443251.1 | c.1948-13_1948-12del | splice_polypyrimidine_tract_variant, intron_variant | ||||
COL5A2 | XM_047443252.1 | c.1948-13_1948-12del | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.2086-13_2086-12del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000393.5 | P1 | |||
COL5A2 | ENST00000618828.1 | c.925-13_925-12del | splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
COL5A2 | ENST00000470524.2 | n.192-13_192-12del | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000891 AC: 133AN: 149268Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0390 AC: 35320AN: 905650Hom.: 0 AF XY: 0.0383 AC XY: 17290AN XY: 450870
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 16, 2018 | 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. - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Computational scores
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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