Variant rs9515218 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001846.4(COL4A2):c.1432+77A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 847,884 control chromosomes in the GnomAD database, including 137,516 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.57 ( 25659 hom., cov: 32)

Exomes 𝑓: 0.55 ( 111857 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.39

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-AS2 (HGNC:39849): (COL4A2 antisense RNA 2)

COL4A2-AS2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 13-110457512-A-G is Benign according to our data. Variant chr13-110457512-A-G is described in ClinVar as [Benign]. Clinvar id is 1249370.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 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.1432+77A>G		intron_variant		ENST00000360467.7
COL4A2-AS2	NR_171022.1 linkuse as main transcript	n.561+13T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
COL4A2	ENST00000360467.7 linkuse as main transcript	c.1432+77A>G	intron_variant	5	NM_001846.4	P1
COL4A2-AS2	ENST00000458403.2 linkuse as main transcript	n.561+13T>C	intron_variant, non_coding_transcript_variant	2
COL4A2	ENST00000617564.2 linkuse as main transcript	c.689+77A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.572

AC:

86896

AN:

151944

Hom.:

25634

Cov.:

show subpopulations

Gnomad AFR

AF:

0.628

Gnomad AMI

AF:

0.677

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.679

Gnomad EAS

AF:

0.225

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.605

Gnomad OTH

AF:

0.579

GnomAD3 exomes

AF:

0.520

AC:

97398

AN:

187482

Hom.:

26543

AF XY:

0.524

AC XY:

53132

AN XY:

101376

show subpopulations

Gnomad AFR exome

AF:

0.636

Gnomad AMR exome

AF:

0.393

Gnomad ASJ exome

AF:

0.669

Gnomad EAS exome

AF:

0.237

Gnomad SAS exome

AF:

0.484

Gnomad FIN exome

AF:

0.444

Gnomad NFE exome

AF:

0.607

Gnomad OTH exome

AF:

0.557

GnomAD4 exome

AF:

0.554

AC:

385330

AN:

695822

Hom.:

111857

Cov.:

AF XY:

0.553

AC XY:

205069

AN XY:

370836

show subpopulations

Gnomad4 AFR exome

AF:

0.632

Gnomad4 AMR exome

AF:

0.399

Gnomad4 ASJ exome

AF:

0.667

Gnomad4 EAS exome

AF:

0.177

Gnomad4 SAS exome

AF:

0.478

Gnomad4 FIN exome

AF:

0.444

Gnomad4 NFE exome

AF:

0.611

Gnomad4 OTH exome

AF:

0.572

GnomAD4 genome

AF:

0.572

AC:

86971

AN:

152062

Hom.:

25659

Cov.:

AF XY:

0.559

AC XY:

41553

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.628

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.679

Gnomad4 EAS

AF:

0.225

Gnomad4 SAS

AF:

0.458

Gnomad4 FIN

AF:

0.430

Gnomad4 NFE

AF:

0.605

Gnomad4 OTH

AF:

0.578

Alfa

AF:

0.594

Hom.:

6737

Bravo

AF:

0.578

Asia WGS

AF:

0.374

AC:

1304

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

-0.92

CADD

Benign

0.24

DANN

Benign

0.30

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