chr13-110504152-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001846.4(COL4A2):c.4290C>T(p.Phe1430Phe) 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

Publications

19 publications found

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:

ENSG00000289010 (HGNC:):

ENSG00000289010 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 1165352.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001846.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL4A2	NM_001846.4	MANE Select	c.4290C>T	p.Phe1430Phe	synonymous	Exon 45 of 48	NP_001837.2
	COL4A2-AS1	NR_046583.1		n.187-1224G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
COL4A2	ENST00000360467.7	TSL:5 MANE Select	c.4290C>T	p.Phe1430Phe	synonymous	Exon 45 of 48	ENSP00000353654.5
COL4A2	ENST00000714399.1		c.4371C>T	p.Phe1457Phe	synonymous	Exon 46 of 49	ENSP00000519666.1
COL4A2	ENST00000400163.8	TSL:5	c.4290C>T	p.Phe1430Phe	synonymous	Exon 45 of 48	ENSP00000383027.4

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

GnomAD2 exomes

AF:

0.986

AC:

245913

AN:

249450

AF XY:

0.989

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 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

African (AFR)

AF:

0.805

AC:

26935

AN:

33474

American (AMR)

AF:

0.990

AC:

44287

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.982

AC:

25670

AN:

26130

East Asian (EAS)

AF:

1.00

AC:

39699

AN:

39700

South Asian (SAS)

AF:

0.999

AC:

86186

AN:

86256

European-Finnish (FIN)

AF:

1.00

AC:

53372

AN:

53380

Middle Eastern (MID)

AF:

0.991

AC:

5714

AN:

5768

European-Non Finnish (NFE)

AF:

0.999

AC:

1111377

AN:

1111966

Other (OTH)

AF:

0.985

AC:

59510

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

440

879

1319

1758

2198

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21662

43324

64986

86648

108310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.946

AC:

144038

AN:

152276

Hom.:

68606

Cov.:

AF XY:

0.948

AC XY:

70554

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.813

AC:

33763

AN:

41534

American (AMR)

AF:

0.983

AC:

15049

AN:

15314

Ashkenazi Jewish (ASJ)

AF:

0.983

AC:

3410

AN:

3470

East Asian (EAS)

AF:

1.00

AC:

5158

AN:

5158

South Asian (SAS)

AF:

0.999

AC:

4824

AN:

4830

European-Finnish (FIN)

AF:

1.00

AC:

10628

AN:

10630

Middle Eastern (MID)

AF:

0.990

AC:

291

AN:

294

European-Non Finnish (NFE)

AF:

0.999

AC:

67965

AN:

68020

Other (OTH)

AF:

0.964

AC:

2038

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

349

697

1046

1394

1743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

not provided

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Porencephaly 2

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

6.9

(source)

DANN

Benign

0.78

PhyloP100

-0.46

PromoterAI

-0.029

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over