Variant 1-36097555-A-AC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_005202.4(COL8A2):c.*13_*14insG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 1,573,498 control chromosomes in the GnomAD database, including 17 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0066 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0013 ( 10 hom. )

Consequence

COL8A2
NM_005202.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.763

Variant links:

Genes affected

COL8A2 (HGNC:2216): (collagen type VIII alpha 2 chain) This gene encodes the alpha 2 chain of type VIII collagen. This protein is a major component of the basement membrane of the corneal endothelium and forms homo- or heterotrimers with alpha 1 (VIII) type collagens. Defects in this gene are associated with Fuchs endothelial corneal dystrophy and posterior polymorphous corneal dystrophy type 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

COL8A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-36097555-A-AC is Benign according to our data. Variant chr1-36097555-A-AC is described in ClinVar as [Likely_benign]. Clinvar id is 1328777.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00656 (995/151570) while in subpopulation AFR AF= 0.0205 (843/41096). AF 95% confidence interval is 0.0194. There are 7 homozygotes in gnomad4. There are 466 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 995 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL8A2	NM_005202.4 linkuse as main transcript	c.13_14insG		3_prime_UTR_variant	4/4	ENST00000397799.2
COL8A2	NM_001294347.2 linkuse as main transcript	c.13_14insG		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
COL8A2	ENST00000397799.2 linkuse as main transcript	c.13_14insG	3_prime_UTR_variant	4/4	5	NM_005202.4	P2
COL8A2	ENST00000481785.1 linkuse as main transcript	c.13_14insG	3_prime_UTR_variant	2/2	1		A2
COL8A2	ENST00000303143.9 linkuse as main transcript	c.13_14insG	3_prime_UTR_variant	2/2	2		P2

Frequencies

GnomAD3 genomes

AF:

0.00656

AC:

993

AN:

151454

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0205

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00303

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.00428

Gnomad SAS

AF:

0.00395

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000221

Gnomad OTH

AF:

0.00432

GnomAD3 exomes

AF:

0.00283

AC:

681

AN:

240424

Hom.:

AF XY:

0.00265

AC XY:

346

AN XY:

130484

show subpopulations

Gnomad AFR exome

AF:

0.0201

Gnomad AMR exome

AF:

0.00228

Gnomad ASJ exome

AF:

0.00844

Gnomad EAS exome

AF:

0.00316

Gnomad SAS exome

AF:

0.00421

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000256

Gnomad OTH exome

AF:

0.00206

GnomAD4 exome

AF:

0.00126

AC:

1787

AN:

1421928

Hom.:

Cov.:

AF XY:

0.00124

AC XY:

874

AN XY:

706034

show subpopulations

Gnomad4 AFR exome

AF:

0.0231

Gnomad4 AMR exome

AF:

0.00249

Gnomad4 ASJ exome

AF:

0.00894

Gnomad4 EAS exome

AF:

0.00181

Gnomad4 SAS exome

AF:

0.00397

Gnomad4 FIN exome

AF:

0.0000579

Gnomad4 NFE exome

AF:

0.000136

Gnomad4 OTH exome

AF:

0.00244

GnomAD4 genome

AF:

0.00656

AC:

995

AN:

151570

Hom.:

Cov.:

AF XY:

0.00629

AC XY:

466

AN XY:

74088

show subpopulations

Gnomad4 AFR

AF:

0.0205

Gnomad4 AMR

AF:

0.00302

Gnomad4 ASJ

AF:

0.0118

Gnomad4 EAS

AF:

0.00429

Gnomad4 SAS

AF:

0.00396

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000221

Gnomad4 OTH

AF:

0.00427

Asia WGS

AF:

0.00462

AC:

AN:

3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over