Variant 13-110504152-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001846.4(COL4A2):c.4290C>T(p.Phe1430=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.989 in 1,614,066 control chromosomes in the GnomAD database, including 791,151 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.95 ( 68606 hom., cov: 33)

Exomes 𝑓: 0.99 ( 722545 hom. )

Consequence

COL4A2
NM_001846.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.463

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 13-110504152-C-T is Benign according to our data. Variant chr13-110504152-C-T is described in ClinVar as [Benign]. Clinvar id is 1165352.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-110504152-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.463 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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.4290C>T	p.Phe1430=	synonymous_variant	45/48	ENST00000360467.7	NP_001837.2
COL4A2-AS1	NR_046583.1 linkuse as main transcript	n.187-1224G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.4290C>T	p.Phe1430=	synonymous_variant	45/48	5	NM_001846.4	ENSP00000353654	P1
COL4A2-AS1	ENST00000417970.2 linkuse as main transcript	n.187-1224G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.946

AC:

143940

AN:

152158

Hom.:

68563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.813

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.983

Gnomad ASJ

AF:

0.983

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.994

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.964

GnomAD3 exomes

AF:

0.986

AC:

245913

AN:

249450

Hom.:

121457

AF XY:

0.989

AC XY:

133865

AN XY:

135340

show subpopulations

Gnomad AFR exome

AF:

0.813

Gnomad AMR exome

AF:

0.991

Gnomad ASJ exome

AF:

0.983

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.999

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.999

Gnomad OTH exome

AF:

0.993

GnomAD4 exome

AF:

0.994

AC:

1452750

AN:

1461790

Hom.:

722545

Cov.:

AF XY:

0.995

AC XY:

723253

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.805

Gnomad4 AMR exome

AF:

0.990

Gnomad4 ASJ exome

AF:

0.982

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.999

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.999

Gnomad4 OTH exome

AF:

0.985

GnomAD4 genome

AF:

0.946

AC:

144038

AN:

152276

Hom.:

68606

Cov.:

AF XY:

0.948

AC XY:

70554

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.813

Gnomad4 AMR

AF:

0.983

Gnomad4 ASJ

AF:

0.983

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.999

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.964

Alfa

AF:

0.973

Hom.:

37395

Bravo

AF:

0.939

Asia WGS

AF:

0.987

AC:

3432

AN:

3478

EpiCase

AF:

0.999

EpiControl

AF:

0.999

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

not provided

Benign:2

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	- -

Porencephaly 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

6.9

DANN

Benign

0.78

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