Variant 3-99762695-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020351.4(COL8A1):c.-4+17674G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0797 in 152,282 control chromosomes in the GnomAD database, including 583 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.080 ( 583 hom., cov: 32)

Consequence

COL8A1
NM_020351.4 intron

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -1.14

Variant links:

Genes affected

COL8A1 (HGNC:2215): (collagen type VIII alpha 1 chain) This gene encodes one of the two alpha chains of type VIII collagen. The gene product is a short chain collagen and a major component of the basement membrane of the corneal endothelium. The type VIII collagen fibril can be either a homo- or a heterotrimer. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Dec 2011]

COL8A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL8A1	NM_020351.4 link	c.-4+17674G>T		intron_variant		ENST00000652472.1	NP_065084.2	P27658
COL8A1	NM_001850.5 link	c.-4+17674G>T		intron_variant			NP_001841.2	P27658

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL8A1	ENST00000652472.1 link	c.-4+17674G>T		intron_variant			NM_020351.4	ENSP00000498483.1		P27658

Frequencies

GnomAD3 genomes

AF:

0.0798

AC:

12142

AN:

152164

Hom.:

584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0456

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.0519

Gnomad ASJ

AF:

0.0378

Gnomad EAS

AF:

0.0331

Gnomad SAS

AF:

0.0903

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0968

Gnomad OTH

AF:

0.0690

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0797

AC:

12131

AN:

152282

Hom.:

583

Cov.:

AF XY:

0.0815

AC XY:

6070

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0454

Gnomad4 AMR

AF:

0.0518

Gnomad4 ASJ

AF:

0.0378

Gnomad4 EAS

AF:

0.0326

Gnomad4 SAS

AF:

0.0899

Gnomad4 FIN

AF:

0.169

Gnomad4 NFE

AF:

0.0968

Gnomad4 OTH

AF:

0.0678

Alfa

AF:

0.0891

Hom.:

1149

Bravo

AF:

0.0683

Asia WGS

AF:

0.0550

AC:

192

AN:

3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not provided

Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.49

DANN

Benign

0.58

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