Variant chr13-110504064-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.4285+71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 1,558,194 control chromosomes in the GnomAD database, including 182,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 15552 hom., cov: 32)

Exomes 𝑓: 0.48 ( 166635 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.40

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-AS1 (HGNC:):

COL4A2-AS1 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=-0.82).

BP6

Variant 13-110504064-G-A is Benign according to our data. Variant chr13-110504064-G-A is described in ClinVar as [Benign]. Clinvar id is 1286277.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 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.4285+71G>A		intron_variant		ENST00000360467.7	NP_001837.2	P08572A0A024RDW8
COL4A2-AS1	NR_046583.1 linkuse as main transcript	n.187-1136C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.4285+71G>A		intron_variant		5	NM_001846.4	ENSP00000353654.5		P08572

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

68092

AN:

151878

Hom.:

15532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.355

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.470

Gnomad ASJ

AF:

0.460

Gnomad EAS

AF:

0.618

Gnomad SAS

AF:

0.528

Gnomad FIN

AF:

0.440

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.479

Gnomad OTH

AF:

0.459

GnomAD4 exome

AF:

0.483

AC:

679840

AN:

1406198

Hom.:

166635

Cov.:

AF XY:

0.485

AC XY:

340024

AN XY:

701306

show subpopulations

Gnomad4 AFR exome

AF:

0.344

Gnomad4 AMR exome

AF:

0.537

Gnomad4 ASJ exome

AF:

0.449

Gnomad4 EAS exome

AF:

0.616

Gnomad4 SAS exome

AF:

0.536

Gnomad4 FIN exome

AF:

0.446

Gnomad4 NFE exome

AF:

0.480

Gnomad4 OTH exome

AF:

0.472

GnomAD4 genome

AF:

0.448

AC:

68151

AN:

151996

Hom.:

15552

Cov.:

AF XY:

0.450

AC XY:

33403

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.355

Gnomad4 AMR

AF:

0.470

Gnomad4 ASJ

AF:

0.460

Gnomad4 EAS

AF:

0.618

Gnomad4 SAS

AF:

0.528

Gnomad4 FIN

AF:

0.440

Gnomad4 NFE

AF:

0.479

Gnomad4 OTH

AF:

0.463

Alfa

AF:

0.459

Hom.:

3905

Bravo

AF:

0.449

Asia WGS

AF:

0.562

AC:

1955

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

-0.82

CADD

Benign

0.20

DANN

Benign

0.77

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