Variant 13-110465637-C-T 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.1978+31C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0782 in 1,552,914 control chromosomes in the GnomAD database, including 6,584 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.075 ( 660 hom., cov: 33)

Exomes 𝑓: 0.079 ( 5924 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.285

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 13-110465637-C-T is Benign according to our data. Variant chr13-110465637-C-T is described in ClinVar as [Benign]. Clinvar id is 1276431.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 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.1978+31C>T		intron_variant		ENST00000360467.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.1978+31C>T		intron_variant		5	NM_001846.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0747

AC:

11365

AN:

152204

Hom.:

652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0256

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.0431

Gnomad FIN

AF:

0.0726

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0717

Gnomad OTH

AF:

0.0865

GnomAD3 exomes

AF:

0.103

AC:

22112

AN:

215038

Hom.:

1799

AF XY:

0.0950

AC XY:

11202

AN XY:

117862

show subpopulations

Gnomad AFR exome

AF:

0.0240

Gnomad AMR exome

AF:

0.255

Gnomad ASJ exome

AF:

0.113

Gnomad EAS exome

AF:

0.220

Gnomad SAS exome

AF:

0.0389

Gnomad FIN exome

AF:

0.0696

Gnomad NFE exome

AF:

0.0735

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.0785

AC:

109982

AN:

1400592

Hom.:

5924

Cov.:

AF XY:

0.0770

AC XY:

53803

AN XY:

698426

show subpopulations

Gnomad4 AFR exome

AF:

0.0207

Gnomad4 AMR exome

AF:

0.239

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.259

Gnomad4 SAS exome

AF:

0.0414

Gnomad4 FIN exome

AF:

0.0693

Gnomad4 NFE exome

AF:

0.0702

Gnomad4 OTH exome

AF:

0.0802

GnomAD4 genome

AF:

0.0747

AC:

11385

AN:

152322

Hom.:

660

Cov.:

AF XY:

0.0753

AC XY:

5609

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0256

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.226

Gnomad4 SAS

AF:

0.0431

Gnomad4 FIN

AF:

0.0726

Gnomad4 NFE

AF:

0.0717

Gnomad4 OTH

AF:

0.0870

Alfa

AF:

0.0821

Hom.:

213

Bravo

AF:

0.0835

Asia WGS

AF:

0.109

AC:

379

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

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.5

DANN

Benign

0.40

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