Variant rs3929758 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001846.4(COL4A2):c.478-75C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 1,468,696 control chromosomes in the GnomAD database, including 394,946 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.75 ( 42870 hom., cov: 32)

Exomes 𝑓: 0.73 ( 352076 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.22

Variant links:

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]

COL4A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 13-110429810-C-A is Benign according to our data. Variant chr13-110429810-C-A is described in ClinVar as [Benign]. Clinvar id is 1241415.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL4A2	NM_001846.4 linkuse as main transcript	c.478-75C>A		intron_variant		ENST00000360467.7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
COL4A2	ENST00000360467.7 linkuse as main transcript	c.478-75C>A	intron_variant		5	NM_001846.4	P1
COL4A2	ENST00000619688.2 linkuse as main transcript	c.*1176C>A	3_prime_UTR_variant	3/3
COL4A2	ENST00000650540.1 linkuse as main transcript	c.478-75C>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113849

AN:

151960

Hom.:

42837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.808

Gnomad AMI

AF:

0.833

Gnomad AMR

AF:

0.720

Gnomad ASJ

AF:

0.742

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.724

Gnomad FIN

AF:

0.786

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.726

Gnomad OTH

AF:

0.746

GnomAD4 exome

AF:

0.730

AC:

961520

AN:

1316618

Hom.:

352076

AF XY:

0.730

AC XY:

482769

AN XY:

661046

show subpopulations

Gnomad4 AFR exome

AF:

0.811

Gnomad4 AMR exome

AF:

0.661

Gnomad4 ASJ exome

AF:

0.759

Gnomad4 EAS exome

AF:

0.613

Gnomad4 SAS exome

AF:

0.723

Gnomad4 FIN exome

AF:

0.776

Gnomad4 NFE exome

AF:

0.732

Gnomad4 OTH exome

AF:

0.734

GnomAD4 genome

AF:

0.749

AC:

113939

AN:

152078

Hom.:

42870

Cov.:

AF XY:

0.751

AC XY:

55813

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.808

Gnomad4 AMR

AF:

0.720

Gnomad4 ASJ

AF:

0.742

Gnomad4 EAS

AF:

0.608

Gnomad4 SAS

AF:

0.724

Gnomad4 FIN

AF:

0.786

Gnomad4 NFE

AF:

0.726

Gnomad4 OTH

AF:

0.744

Alfa

AF:

0.722

Hom.:

12429

Bravo

AF:

0.746

Asia WGS

AF:

0.688

AC:

2394

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.045

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over