Variant 13-110503364-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.4040-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,591,204 control chromosomes in the GnomAD database, including 107,309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 10803 hom., cov: 34)

Exomes 𝑓: 0.36 ( 96506 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.484

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-AS1 (HGNC:40156): (COL4A2 antisense RNA 1)

COL4A2-AS1 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=-0.81).

BP6

Variant 13-110503364-C-T is Benign according to our data. Variant chr13-110503364-C-T is described in ClinVar as [Benign]. Clinvar id is 1165076.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-110503364-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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.4040-19C>T		intron_variant		ENST00000360467.7	NP_001837.2
COL4A2-AS1	NR_046583.1 linkuse as main transcript	n.187-436G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
COL4A2	ENST00000360467.7 linkuse as main transcript	c.4040-19C>T	intron_variant	5	NM_001846.4	ENSP00000353654	P1
COL4A2-AS1	ENST00000417970.2 linkuse as main transcript	n.187-436G>A	intron_variant, non_coding_transcript_variant	3
COL4A2	ENST00000650225.1 linkuse as main transcript	n.1695-19C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.374

AC:

56828

AN:

151988

Hom.:

10796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.269

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.417

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.370

GnomAD3 exomes

AF:

0.347

AC:

76131

AN:

219220

Hom.:

13626

AF XY:

0.354

AC XY:

42189

AN XY:

119310

show subpopulations

Gnomad AFR exome

AF:

0.425

Gnomad AMR exome

AF:

0.226

Gnomad ASJ exome

AF:

0.349

Gnomad EAS exome

AF:

0.205

Gnomad SAS exome

AF:

0.379

Gnomad FIN exome

AF:

0.427

Gnomad NFE exome

AF:

0.370

Gnomad OTH exome

AF:

0.367

GnomAD4 exome

AF:

0.363

AC:

521770

AN:

1439098

Hom.:

96506

Cov.:

AF XY:

0.364

AC XY:

259933

AN XY:

714638

show subpopulations

Gnomad4 AFR exome

AF:

0.432

Gnomad4 AMR exome

AF:

0.233

Gnomad4 ASJ exome

AF:

0.349

Gnomad4 EAS exome

AF:

0.183

Gnomad4 SAS exome

AF:

0.375

Gnomad4 FIN exome

AF:

0.420

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.368

GnomAD4 genome

AF:

0.374

AC:

56861

AN:

152106

Hom.:

10803

Cov.:

AF XY:

0.374

AC XY:

27775

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.424

Gnomad4 AMR

AF:

0.301

Gnomad4 ASJ

AF:

0.342

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.386

Gnomad4 FIN

AF:

0.417

Gnomad4 NFE

AF:

0.368

Gnomad4 OTH

AF:

0.368

Alfa

AF:

0.368

Hom.:

13236

Bravo

AF:

0.363

Asia WGS

AF:

0.295

AC:

1028

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
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

-0.81

CADD

Benign

0.060

DANN

Benign

0.66

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