Variant rs3074455 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001846.4(COL4A2):c.*102dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00053 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0060 ( 0 hom. )

Consequence

COL4A2
NM_001846.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

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 -8 ACMG points.

BS1

Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.00605 (7126/1178400) while in subpopulation EAS AF= 0.0188 (520/27722). AF 95% confidence interval is 0.0174. There are 0 homozygotes in gnomad4_exome. There are 3498 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High AC in GnomAd4 at 79 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL4A2	NM_001846.4 linkuse as main transcript	c.*102dup		3_prime_UTR_variant	48/48	ENST00000360467.7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
COL4A2	ENST00000360467.7 linkuse as main transcript	c.*102dup	3_prime_UTR_variant	48/48	5	NM_001846.4	P1
COL4A2	ENST00000648222.1 linkuse as main transcript	n.929dup	non_coding_transcript_exon_variant	1/1
COL4A2	ENST00000650225.1 linkuse as main transcript	n.2896dup	non_coding_transcript_exon_variant	19/19

Frequencies

GnomAD3 genomes

AF:

0.000521

AC:

AN:

149648

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000664

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000786

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000100

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000193

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00605

AC:

7126

AN:

1178400

Hom.:

Cov.:

AF XY:

0.00609

AC XY:

3498

AN XY:

574750

show subpopulations

Gnomad4 AFR exome

AF:

0.00776

Gnomad4 AMR exome

AF:

0.00863

Gnomad4 ASJ exome

AF:

0.00546

Gnomad4 EAS exome

AF:

0.0188

Gnomad4 SAS exome

AF:

0.00791

Gnomad4 FIN exome

AF:

0.00631

Gnomad4 NFE exome

AF:

0.00544

Gnomad4 OTH exome

AF:

0.00636

GnomAD4 genome

AF:

0.000528

AC:

AN:

149754

Hom.:

Cov.:

AF XY:

0.000521

AC XY:

AN XY:

73004

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.000663

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000789

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000100

Gnomad4 NFE

AF:

0.000193

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over