Variant 13-110485628-G-T 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.3026-27G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 1,569,564 control chromosomes in the GnomAD database, including 2,694 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.052 ( 231 hom., cov: 32)

Exomes 𝑓: 0.057 ( 2463 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.273

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:

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=-0.83).

BP6

Variant 13-110485628-G-T is Benign according to our data. Variant chr13-110485628-G-T is described in ClinVar as [Benign]. Clinvar id is 1228626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-110485628-G-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL4A2	NM_001846.4 link	c.3026-27G>T		intron_variant		ENST00000360467.7	NP_001837.2	P08572A0A024RDW8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A2	ENST00000360467.7 link	c.3026-27G>T		intron_variant		5	NM_001846.4	ENSP00000353654.5		P08572
COL4A2	ENST00000650225.1 link	n.681-27G>T		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0518

AC:

7880

AN:

151988

Hom.:

231

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0321

Gnomad AMI

AF:

0.0308

Gnomad AMR

AF:

0.0649

Gnomad ASJ

AF:

0.0522

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0470

Gnomad FIN

AF:

0.0688

Gnomad MID

AF:

0.102

Gnomad NFE

AF:

0.0627

Gnomad OTH

AF:

0.0488

GnomAD3 exomes

AF:

0.0528

AC:

11642

AN:

220630

Hom.:

362

AF XY:

0.0538

AC XY:

6504

AN XY:

120920

show subpopulations

Gnomad AFR exome

AF:

0.0306

Gnomad AMR exome

AF:

0.0608

Gnomad ASJ exome

AF:

0.0523

Gnomad EAS exome

AF:

0.000184

Gnomad SAS exome

AF:

0.0436

Gnomad FIN exome

AF:

0.0751

Gnomad NFE exome

AF:

0.0594

Gnomad OTH exome

AF:

0.0672

GnomAD4 exome

AF:

0.0567

AC:

80379

AN:

1417464

Hom.:

2463

Cov.:

AF XY:

0.0568

AC XY:

39923

AN XY:

702460

show subpopulations

Gnomad4 AFR exome

AF:

0.0337

Gnomad4 AMR exome

AF:

0.0625

Gnomad4 ASJ exome

AF:

0.0574

Gnomad4 EAS exome

AF:

0.0000512

Gnomad4 SAS exome

AF:

0.0452

Gnomad4 FIN exome

AF:

0.0720

Gnomad4 NFE exome

AF:

0.0592

Gnomad4 OTH exome

AF:

0.0573

GnomAD4 genome

AF:

0.0519

AC:

7890

AN:

152100

Hom.:

231

Cov.:

AF XY:

0.0513

AC XY:

3817

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.0323

Gnomad4 AMR

AF:

0.0648

Gnomad4 ASJ

AF:

0.0522

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0473

Gnomad4 FIN

AF:

0.0688

Gnomad4 NFE

AF:

0.0627

Gnomad4 OTH

AF:

0.0487

Alfa

AF:

0.0594

Hom.:

Bravo

AF:

0.0496

Asia WGS

AF:

0.0270

AC:

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

-0.83

CADD

Benign

0.41

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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