Variant 13-110492218-C-T 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.3562+41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,527,260 control chromosomes in the GnomAD database, including 18,380 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2627 hom., cov: 33)

Exomes 𝑓: 0.14 ( 15753 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.63

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=-0.89).

BP6

Variant 13-110492218-C-T is Benign according to our data. Variant chr13-110492218-C-T is described in ClinVar as [Benign]. Clinvar id is 1178451.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 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.3562+41C>T		intron_variant		ENST00000360467.7	NP_001837.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.3562+41C>T		intron_variant		5	NM_001846.4	ENSP00000353654	P1
COL4A2	ENST00000650225.1 linkuse as main transcript	n.1217+41C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27057

AN:

152060

Hom.:

2623

Cov.:

show subpopulations

Gnomad AFR

AF:

0.240

Gnomad AMI

AF:

0.0703

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.169

GnomAD3 exomes

AF:

0.167

AC:

25321

AN:

151842

Hom.:

2374

AF XY:

0.171

AC XY:

13734

AN XY:

80546

show subpopulations

Gnomad AFR exome

AF:

0.250

Gnomad AMR exome

AF:

0.0978

Gnomad ASJ exome

AF:

0.192

Gnomad EAS exome

AF:

0.158

Gnomad SAS exome

AF:

0.229

Gnomad FIN exome

AF:

0.263

Gnomad NFE exome

AF:

0.133

Gnomad OTH exome

AF:

0.157

GnomAD4 exome

AF:

0.145

AC:

199020

AN:

1375082

Hom.:

15753

Cov.:

AF XY:

0.147

AC XY:

99893

AN XY:

679702

show subpopulations

Gnomad4 AFR exome

AF:

0.249

Gnomad4 AMR exome

AF:

0.103

Gnomad4 ASJ exome

AF:

0.195

Gnomad4 EAS exome

AF:

0.188

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.259

Gnomad4 NFE exome

AF:

0.128

Gnomad4 OTH exome

AF:

0.157

GnomAD4 genome

AF:

0.178

AC:

27089

AN:

152178

Hom.:

2627

Cov.:

AF XY:

0.183

AC XY:

13607

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.241

Gnomad4 AMR

AF:

0.138

Gnomad4 ASJ

AF:

0.191

Gnomad4 EAS

AF:

0.171

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.260

Gnomad4 NFE

AF:

0.133

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.164

Hom.:

439

Bravo

AF:

0.168

Asia WGS

AF:

0.182

AC:

630

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

-0.89

CADD

Benign

0.62

DANN

Benign

0.65

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