chr3-99777507-G-T

Position:

• chr3-99777507-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020351.4(COL8A1):​c.-3-13173G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,048 control chromosomes in the GnomAD database, including 4,045 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (4045 hom., cov: 32)
• Consequence: COL8A1 NM_020351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL8A1	NM_020351.4	c.-3-13173G>T		intron_variant		ENST00000652472.1
COL8A1	NM_001850.5	c.-3-13173G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL8A1	ENST00000652472.1	c.-3-13173G>T		intron_variant			NM_020351.4	P1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32762 AN: 151928 Hom.: 4035 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.216 AC: 32788 AN: 152048 Hom.: 4045 Cov.: 32 AF XY: 0.218 AC XY: 16190 AN XY: 74342

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0796

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.181

Alfa AF: 0.159 Hom.: 971

Bravo AF: 0.208

Asia WGS AF: 0.187 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.6
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs7614366; hg19: chr3-99496351;