Variant chr13-110485908-G-A 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.3207+72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,581,824 control chromosomes in the GnomAD database, including 14,549 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1400 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13149 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0290

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 13-110485908-G-A is Benign according to our data. Variant chr13-110485908-G-A is described in ClinVar as [Benign]. Clinvar id is 1229583.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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.3207+72G>A		intron_variant		ENST00000360467.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.3207+72G>A		intron_variant		5	NM_001846.4	P1
COL4A2	ENST00000650225.1 linkuse as main transcript	n.862+72G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20623

AN:

152066

Hom.:

1397

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.134

AC:

191168

AN:

1429640

Hom.:

13149

AF XY:

0.133

AC XY:

94103

AN XY:

709254

show subpopulations

Gnomad4 AFR exome

AF:

0.161

Gnomad4 AMR exome

AF:

0.125

Gnomad4 ASJ exome

AF:

0.0996

Gnomad4 EAS exome

AF:

0.113

Gnomad4 SAS exome

AF:

0.120

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.137

Gnomad4 OTH exome

AF:

0.129

GnomAD4 genome

AF:

0.136

AC:

20645

AN:

152184

Hom.:

1400

Cov.:

AF XY:

0.135

AC XY:

10068

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.109

Gnomad4 ASJ

AF:

0.110

Gnomad4 EAS

AF:

0.156

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.132

Hom.:

2405

Bravo

AF:

0.138

Asia WGS

AF:

0.117

AC:

408

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 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.0

DANN

Benign

0.61

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