Variant chr13-110449584-C-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.1079-95C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,203,346 control chromosomes in the GnomAD database, including 69,512 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 7101 hom., cov: 33)

Exomes 𝑓: 0.34 ( 62411 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.243

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=-0.9).

BP6

Variant 13-110449584-C-T is Benign according to our data. Variant chr13-110449584-C-T is described in ClinVar as [Benign]. Clinvar id is 1258504.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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.1079-95C>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.1079-95C>T		intron_variant		5	NM_001846.4	P1
COL4A2	ENST00000617564.2 linkuse as main transcript	c.336-95C>T		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43354

AN:

152048

Hom.:

7096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.265

GnomAD4 exome

AF:

0.340

AC:

357197

AN:

1051180

Hom.:

62411

AF XY:

0.342

AC XY:

177752

AN XY:

520458

show subpopulations

Gnomad4 AFR exome

AF:

0.118

Gnomad4 AMR exome

AF:

0.185

Gnomad4 ASJ exome

AF:

0.254

Gnomad4 EAS exome

AF:

0.266

Gnomad4 SAS exome

AF:

0.331

Gnomad4 FIN exome

AF:

0.404

Gnomad4 NFE exome

AF:

0.355

Gnomad4 OTH exome

AF:

0.309

GnomAD4 genome

AF:

0.285

AC:

43361

AN:

152166

Hom.:

7101

Cov.:

AF XY:

0.285

AC XY:

21235

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.133

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.273

Gnomad4 EAS

AF:

0.269

Gnomad4 SAS

AF:

0.324

Gnomad4 FIN

AF:

0.405

Gnomad4 NFE

AF:

0.375

Gnomad4 OTH

AF:

0.261

Alfa

AF:

0.326

Hom.:

2015

Bravo

AF:

0.259

Asia WGS

AF:

0.277

AC:

966

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

-0.90

CADD

Benign

0.85

DANN

Benign

0.63

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