Variant rs9301460 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.4139-41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 1,609,432 control chromosomes in the GnomAD database, including 110,353 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 11531 hom., cov: 32)

Exomes 𝑓: 0.36 ( 98822 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.01

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=-0.8).

BP6

Variant 13-110503806-G-A is Benign according to our data. Variant chr13-110503806-G-A is described in ClinVar as [Benign]. Clinvar id is 1281130.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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.4139-41G>A		intron_variant		ENST00000360467.7	NP_001837.2	P08572A0A024RDW8
COL4A2-AS1	NR_046583.1 linkuse as main transcript	n.187-878C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.4139-41G>A		intron_variant		5	NM_001846.4	ENSP00000353654.5		P08572

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

58431

AN:

151852

Hom.:

11520

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.353

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.415

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.376

GnomAD3 exomes

AF:

0.348

AC:

86375

AN:

248350

Hom.:

15919

AF XY:

0.354

AC XY:

47738

AN XY:

134862

show subpopulations

Gnomad AFR exome

AF:

0.459

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.356

Gnomad EAS exome

AF:

0.201

Gnomad SAS exome

AF:

0.378

Gnomad FIN exome

AF:

0.425

Gnomad NFE exome

AF:

0.369

Gnomad OTH exome

AF:

0.366

GnomAD4 exome

AF:

0.364

AC:

529898

AN:

1457462

Hom.:

98822

Cov.:

AF XY:

0.365

AC XY:

264575

AN XY:

725280

show subpopulations

Gnomad4 AFR exome

AF:

0.468

Gnomad4 AMR exome

AF:

0.232

Gnomad4 ASJ exome

AF:

0.359

Gnomad4 EAS exome

AF:

0.182

Gnomad4 SAS exome

AF:

0.376

Gnomad4 FIN exome

AF:

0.420

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.371

GnomAD4 genome

AF:

0.385

AC:

58471

AN:

151970

Hom.:

11531

Cov.:

AF XY:

0.384

AC XY:

28534

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.459

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.353

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.387

Gnomad4 FIN

AF:

0.415

Gnomad4 NFE

AF:

0.369

Gnomad4 OTH

AF:

0.373

Alfa

AF:

0.382

Hom.:

2517

Bravo

AF:

0.375

Asia WGS

AF:

0.296

AC:

1031

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

-0.80

CADD

Benign

3.8

DANN

Benign

0.55

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