rs7992330
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001846.4(COL4A2):c.1776+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,609,344 control chromosomes in the GnomAD database, including 62,881 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4444 hom., cov: 33)
Exomes 𝑓: 0.28 ( 58437 hom. )
Consequence
COL4A2
NM_001846.4 intron
NM_001846.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.302
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 13-110462404-G-A is Benign according to our data. Variant chr13-110462404-G-A is described in ClinVar as [Benign]. Clinvar id is 1165077.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-110462404-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A2 | NM_001846.4 | c.1776+20G>A | intron_variant | ENST00000360467.7 | |||
COL4A2-AS2 | NR_171022.1 | n.265+619C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A2 | ENST00000360467.7 | c.1776+20G>A | intron_variant | 5 | NM_001846.4 | P1 | |||
COL4A2-AS2 | ENST00000458403.2 | n.265+619C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
COL4A2 | ENST00000478681.1 | n.292G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.228 AC: 34659AN: 152090Hom.: 4444 Cov.: 33
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GnomAD3 exomes AF: 0.231 AC: 56185AN: 242810Hom.: 7176 AF XY: 0.238 AC XY: 31651AN XY: 132770
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GnomAD4 exome AF: 0.277 AC: 403539AN: 1457136Hom.: 58437 Cov.: 32 AF XY: 0.277 AC XY: 200672AN XY: 724980
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GnomAD4 genome ? AF: 0.228 AC: 34661AN: 152208Hom.: 4444 Cov.: 33 AF XY: 0.224 AC XY: 16651AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
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