Variant 13-110493329-G-C 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.3634+47G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 1,597,572 control chromosomes in the GnomAD database, including 238,977 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 16864 hom., cov: 32)

Exomes 𝑓: 0.55 ( 222113 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.465

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:

COL4A2 (HGNC:):

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=-0.9).

BP6

Variant 13-110493329-G-C is Benign according to our data. Variant chr13-110493329-G-C is described in ClinVar as [Benign]. Clinvar id is 1289388.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL4A2	NM_001846.4 linkuse as main transcript	c.3634+47G>C		intron_variant		ENST00000360467.7	NP_001837.2	P08572A0A024RDW8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.3634+47G>C		intron_variant		5	NM_001846.4	ENSP00000353654.5		P08572
COL4A2	ENST00000650225.1 linkuse as main transcript	n.1289+47G>C		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66934

AN:

151958

Hom.:

16860

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.488

Gnomad ASJ

AF:

0.478

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.482

Gnomad FIN

AF:

0.488

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.460

GnomAD3 exomes

AF:

0.516

AC:

126383

AN:

245128

Hom.:

33684

AF XY:

0.520

AC XY:

69332

AN XY:

133288

show subpopulations

Gnomad AFR exome

AF:

0.167

Gnomad AMR exome

AF:

0.511

Gnomad ASJ exome

AF:

0.482

Gnomad EAS exome

AF:

0.576

Gnomad SAS exome

AF:

0.491

Gnomad FIN exome

AF:

0.490

Gnomad NFE exome

AF:

0.569

Gnomad OTH exome

AF:

0.532

GnomAD4 exome

AF:

0.549

AC:

793864

AN:

1445494

Hom.:

222113

Cov.:

AF XY:

0.549

AC XY:

395220

AN XY:

719906

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.512

Gnomad4 ASJ exome

AF:

0.480

Gnomad4 EAS exome

AF:

0.555

Gnomad4 SAS exome

AF:

0.493

Gnomad4 FIN exome

AF:

0.492

Gnomad4 NFE exome

AF:

0.573

Gnomad4 OTH exome

AF:

0.521

GnomAD4 genome

AF:

0.440

AC:

66950

AN:

152078

Hom.:

16864

Cov.:

AF XY:

0.441

AC XY:

32744

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.488

Gnomad4 ASJ

AF:

0.478

Gnomad4 EAS

AF:

0.561

Gnomad4 SAS

AF:

0.482

Gnomad4 FIN

AF:

0.488

Gnomad4 NFE

AF:

0.567

Gnomad4 OTH

AF:

0.462

Alfa

AF:

0.424

Hom.:

2258

Bravo

AF:

0.431

Asia WGS

AF:

0.540

AC:

1879

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	Jul 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.6

DANN

Benign

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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