Variant rs7984100 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.862-41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 1,612,218 control chromosomes in the GnomAD database, including 73,930 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 9846 hom., cov: 33)

Exomes 𝑓: 0.29 ( 64084 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.29

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=-0.91).

BP6

Variant 13-110438577-G-A is Benign according to our data. Variant chr13-110438577-G-A is described in ClinVar as [Benign]. Clinvar id is 1217363.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-110438577-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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.862-41G>A		intron_variant		ENST00000360467.7	NP_001837.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
COL4A2	ENST00000360467.7 linkuse as main transcript	c.862-41G>A	intron_variant	5	NM_001846.4	ENSP00000353654	P1
COL4A2	ENST00000617564.2 linkuse as main transcript	c.119-41G>A	intron_variant			ENSP00000481492
COL4A2	ENST00000650540.1 linkuse as main transcript	c.862-41G>A	intron_variant			ENSP00000497878

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52318

AN:

151794

Hom.:

9838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.509

Gnomad AMI

AF:

0.239

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.413

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.346

GnomAD3 exomes

AF:

0.282

AC:

70299

AN:

249442

Hom.:

11100

AF XY:

0.280

AC XY:

37829

AN XY:

135330

show subpopulations

Gnomad AFR exome

AF:

0.521

Gnomad AMR exome

AF:

0.193

Gnomad ASJ exome

AF:

0.433

Gnomad EAS exome

AF:

0.145

Gnomad SAS exome

AF:

0.222

Gnomad FIN exome

AF:

0.294

Gnomad NFE exome

AF:

0.297

Gnomad OTH exome

AF:

0.304

GnomAD4 exome

AF:

0.289

AC:

422118

AN:

1460306

Hom.:

64084

Cov.:

AF XY:

0.287

AC XY:

208704

AN XY:

726538

show subpopulations

Gnomad4 AFR exome

AF:

0.517

Gnomad4 AMR exome

AF:

0.205

Gnomad4 ASJ exome

AF:

0.427

Gnomad4 EAS exome

AF:

0.116

Gnomad4 SAS exome

AF:

0.224

Gnomad4 FIN exome

AF:

0.289

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.310

GnomAD4 genome

AF:

0.345

AC:

52357

AN:

151912

Hom.:

9846

Cov.:

AF XY:

0.339

AC XY:

25192

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.508

Gnomad4 AMR

AF:

0.288

Gnomad4 ASJ

AF:

0.413

Gnomad4 EAS

AF:

0.127

Gnomad4 SAS

AF:

0.207

Gnomad4 FIN

AF:

0.286

Gnomad4 NFE

AF:

0.291

Gnomad4 OTH

AF:

0.347

Alfa

AF:

0.262

Hom.:

1392

Bravo

AF:

0.359

ClinVar

Significance: Benign

Submissions summary: Benign:3

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	- -

Porencephaly 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.010

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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