Variant 13-110436109-A-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.727-160A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 1,071,630 control chromosomes in the GnomAD database, including 1,682 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.040 ( 167 hom., cov: 32)

Exomes 𝑓: 0.050 ( 1515 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.30

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=-0.91).

BP6

Variant 13-110436109-A-T is Benign according to our data. Variant chr13-110436109-A-T is described in ClinVar as [Benign]. Clinvar id is 1278604.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 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.727-160A>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 linkuse as main transcript	c.727-160A>T		intron_variant		5	NM_001846.4	ENSP00000353654.5		P08572
COL4A2	ENST00000650540.1 linkuse as main transcript	c.727-160A>T		intron_variant				ENSP00000497878.1		A0A3B3ITQ8

Frequencies

GnomAD3 genomes

AF:

0.0397

AC:

5989

AN:

150790

Hom.:

167

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00876

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0301

Gnomad ASJ

AF:

0.0282

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.0716

Gnomad FIN

AF:

0.0699

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0467

Gnomad OTH

AF:

0.0436

GnomAD3 exomes

AF:

0.0515

AC:

11401

AN:

221416

Hom.:

442

AF XY:

0.0530

AC XY:

6430

AN XY:

121432

show subpopulations

Gnomad AFR exome

AF:

0.00861

Gnomad AMR exome

AF:

0.0247

Gnomad ASJ exome

AF:

0.0252

Gnomad EAS exome

AF:

0.141

Gnomad SAS exome

AF:

0.0737

Gnomad FIN exome

AF:

0.0653

Gnomad NFE exome

AF:

0.0457

Gnomad OTH exome

AF:

0.0472

GnomAD4 exome

AF:

0.0497

AC:

45746

AN:

920726

Hom.:

1515

Cov.:

AF XY:

0.0505

AC XY:

24070

AN XY:

476754

show subpopulations

Gnomad4 AFR exome

AF:

0.00750

Gnomad4 AMR exome

AF:

0.0251

Gnomad4 ASJ exome

AF:

0.0252

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.0717

Gnomad4 FIN exome

AF:

0.0601

Gnomad4 NFE exome

AF:

0.0447

Gnomad4 OTH exome

AF:

0.0461

GnomAD4 genome

AF:

0.0397

AC:

5988

AN:

150904

Hom.:

167

Cov.:

AF XY:

0.0411

AC XY:

3028

AN XY:

73758

show subpopulations

Gnomad4 AFR

AF:

0.00873

Gnomad4 AMR

AF:

0.0300

Gnomad4 ASJ

AF:

0.0282

Gnomad4 EAS

AF:

0.140

Gnomad4 SAS

AF:

0.0717

Gnomad4 FIN

AF:

0.0699

Gnomad4 NFE

AF:

0.0467

Gnomad4 OTH

AF:

0.0427

Alfa

AF:

0.0380

Hom.:

Bravo

AF:

0.0353

Asia WGS

AF:

0.0970

AC:

338

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

-0.91

CADD

Benign

0.13

DANN

Benign

0.57

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