rs74967960
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001846.4(COL4A2):c.315+19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0094 in 1,614,086 control chromosomes in the GnomAD database, including 245 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.025 ( 92 hom., cov: 34)
Exomes 𝑓: 0.0078 ( 153 hom. )
Consequence
COL4A2
NM_001846.4 intron
NM_001846.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.11
Genes affected
COL4A2 (HGNC:2203): (collagen type IV alpha 2 chain) This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. The C-terminal portion of the protein, known as canstatin, is an inhibitor of angiogenesis and tumor growth. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. [provided by RefSeq, Jul 2008]
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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=-0.84).
BP6
?
Variant 13-110424887-T-C is Benign according to our data. Variant chr13-110424887-T-C is described in ClinVar as [Benign]. Clinvar id is 1280685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-110424887-T-C is described in Lovd as [Benign]. Variant chr13-110424887-T-C is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0693 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A2 | NM_001846.4 | c.315+19T>C | intron_variant | ENST00000360467.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A2 | ENST00000360467.7 | c.315+19T>C | intron_variant | 5 | NM_001846.4 | P1 | |||
COL4A2 | ENST00000619688.2 | c.67+19T>C | intron_variant | ||||||
COL4A2 | ENST00000650540.1 | c.315+19T>C | intron_variant | ||||||
COL4A2 | ENST00000400163.7 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0248 AC: 3770AN: 152154Hom.: 92 Cov.: 34
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GnomAD3 exomes AF: 0.00944 AC: 2355AN: 249500Hom.: 47 AF XY: 0.00796 AC XY: 1077AN XY: 135368
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GnomAD4 exome AF: 0.00780 AC: 11402AN: 1461814Hom.: 153 Cov.: 38 AF XY: 0.00750 AC XY: 5455AN XY: 727214
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GnomAD4 genome ? AF: 0.0248 AC: 3774AN: 152272Hom.: 92 Cov.: 34 AF XY: 0.0244 AC XY: 1818AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 10, 2018 | - - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
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