Variant rs9559814 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.2096-81A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 1,492,644 control chromosomes in the GnomAD database, including 265,348 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.60 ( 28263 hom., cov: 33)

Exomes 𝑓: 0.59 ( 237085 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.45

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 13-110469136-A-G is Benign according to our data. Variant chr13-110469136-A-G is described in ClinVar as [Benign]. Clinvar id is 1274675.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 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.2096-81A>G		intron_variant		ENST00000360467.7	NP_001837.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.2096-81A>G		intron_variant		5	NM_001846.4	ENSP00000353654	P1
COL4A2	ENST00000494852.2 linkuse as main transcript	c.16-81A>G		intron_variant		3		ENSP00000497664

Frequencies

GnomAD3 genomes

AF:

0.600

AC:

91235

AN:

151996

Hom.:

28230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.698

Gnomad AMI

AF:

0.670

Gnomad AMR

AF:

0.501

Gnomad ASJ

AF:

0.679

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.465

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.606

GnomAD4 exome

AF:

0.589

AC:

789142

AN:

1340530

Hom.:

237085

AF XY:

0.585

AC XY:

387239

AN XY:

661568

show subpopulations

Gnomad4 AFR exome

AF:

0.712

Gnomad4 AMR exome

AF:

0.425

Gnomad4 ASJ exome

AF:

0.660

Gnomad4 EAS exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.478

Gnomad4 FIN exome

AF:

0.478

Gnomad4 NFE exome

AF:

0.614

Gnomad4 OTH exome

AF:

0.588

GnomAD4 genome

AF:

0.600

AC:

91326

AN:

152114

Hom.:

28263

Cov.:

AF XY:

0.588

AC XY:

43742

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.699

Gnomad4 AMR

AF:

0.500

Gnomad4 ASJ

AF:

0.679

Gnomad4 EAS

AF:

0.289

Gnomad4 SAS

AF:

0.457

Gnomad4 FIN

AF:

0.465

Gnomad4 NFE

AF:

0.612

Gnomad4 OTH

AF:

0.606

Alfa

AF:

0.534

Hom.:

2723

Bravo

AF:

0.607

Asia WGS

AF:

0.401

AC:

1396

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	Jun 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.026

DANN

Benign

0.47

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