rs59905747
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001846.4(COL4A2):c.1012-100C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 978,070 control chromosomes in the GnomAD database, including 4,871 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.090 ( 748 hom., cov: 33)
Exomes 𝑓: 0.084 ( 4123 hom. )
Consequence
COL4A2
NM_001846.4 intron
NM_001846.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.186
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]
Genome browser will be placed here
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 13-110446698-C-G is Benign according to our data. Variant chr13-110446698-C-G is described in ClinVar as [Benign]. Clinvar id is 1231605.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A2 | NM_001846.4 | c.1012-100C>G | intron_variant | ENST00000360467.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A2 | ENST00000360467.7 | c.1012-100C>G | intron_variant | 5 | NM_001846.4 | P1 | |||
COL4A2 | ENST00000617564.2 | c.269-100C>G | intron_variant | ||||||
COL4A2 | ENST00000650540.1 | c.1012-100C>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0896 AC: 13625AN: 152104Hom.: 739 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
13625
AN:
152104
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0841 AC: 69451AN: 825848Hom.: 4123 AF XY: 0.0818 AC XY: 34751AN XY: 424912
GnomAD4 exome
AF:
AC:
69451
AN:
825848
Hom.:
AF XY:
AC XY:
34751
AN XY:
424912
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0897 AC: 13661AN: 152222Hom.: 748 Cov.: 33 AF XY: 0.0902 AC XY: 6712AN XY: 74430
GnomAD4 genome
?
AF:
AC:
13661
AN:
152222
Hom.:
Cov.:
33
AF XY:
AC XY:
6712
AN XY:
74430
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
459
AN:
3478
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 | GeneDx | Jul 09, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at