Variant chr13-110457229-G-C 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.1340-114G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.081 ( 297 hom., cov: 0)

Exomes 𝑓: 0.089 ( 2063 hom. )

Failed GnomAD Quality Control

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.360

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-AS2 (HGNC:39849): (COL4A2 antisense RNA 2)

COL4A2-AS2 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=-0.92).

BP6

Variant 13-110457229-G-C is Benign according to our data. Variant chr13-110457229-G-C is described in ClinVar as [Benign]. Clinvar id is 1275047.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL4A2	NM_001846.4 link	c.1340-114G>C		intron_variant		ENST00000360467.7	NP_001837.2	P08572A0A024RDW8
COL4A2-AS2	NR_171022.1 link	n.689C>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
COL4A2	ENST00000360467.7 link	c.1340-114G>C	intron_variant		5	NM_001846.4	ENSP00000353654.5	P08572
COL4A2	ENST00000617564.2 link	c.596-114G>C	intron_variant		6		ENSP00000481492.3	A0A087WY39
COL4A2-AS2	ENST00000458403.2 link	n.689C>G	non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes

AF:

0.0814

AC:

2533

AN:

31122

Hom.:

297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0744

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0793

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.00756

Gnomad SAS

AF:

0.0462

Gnomad FIN

AF:

0.0365

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.0691

GnomAD3 exomes

AF:

0.0193

AC:

750

AN:

38958

Hom.:

AF XY:

0.0174

AC XY:

376

AN XY:

21568

show subpopulations

Gnomad AFR exome

AF:

0.0684

Gnomad AMR exome

AF:

0.0172

Gnomad ASJ exome

AF:

0.0173

Gnomad EAS exome

AF:

0.00932

Gnomad SAS exome

AF:

0.00714

Gnomad FIN exome

AF:

0.00317

Gnomad NFE exome

AF:

0.0276

Gnomad OTH exome

AF:

0.0329

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0888

AC:

12426

AN:

139934

Hom.:

2063

Cov.:

AF XY:

0.0851

AC XY:

6444

AN XY:

75736

show subpopulations

Gnomad4 AFR exome

AF:

0.129

Gnomad4 AMR exome

AF:

0.0542

Gnomad4 ASJ exome

AF:

0.190

Gnomad4 EAS exome

AF:

0.00802

Gnomad4 SAS exome

AF:

0.0292

Gnomad4 FIN exome

AF:

0.0765

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

AF:

0.0814

AC:

2534

AN:

31142

Hom.:

297

Cov.:

AF XY:

0.0782

AC XY:

1202

AN XY:

15372

show subpopulations

Gnomad4 AFR

AF:

0.0748

Gnomad4 AMR

AF:

0.0789

Gnomad4 ASJ

AF:

0.174

Gnomad4 EAS

AF:

0.00761

Gnomad4 SAS

AF:

0.0461

Gnomad4 FIN

AF:

0.0365

Gnomad4 NFE

AF:

0.107

Gnomad4 OTH

AF:

0.0707

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	clinical testing	GeneDx	Jun 29, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.3

DANN

Benign

0.88

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