5-178320690-T-C

Variant summary

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

The NM_173465.4(COL23A1):c.362-13771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,182 control chromosomes in the GnomAD database, including 2,434 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.15 (2434 hom., cov: 33)
• Consequence: COL23A1 NM_173465.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -1.88

Genes affected

COL23A1 (HGNC:22990): (collagen type XXIII alpha 1 chain) COL23A1 is a member of the transmembrane collagens, a subfamily of the nonfibrillar collagens that contain a single pass hydrophobic transmembrane domain (Banyard et al., 2003 [PubMed 12644459]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL23A1	NM_173465.4	c.362-13771A>G		intron_variant		ENST00000390654.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL23A1	ENST00000390654.8	c.362-13771A>G		intron_variant		5	NM_173465.4	P1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22656 AN: 152064 Hom.: 2433 Cov.: 33

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.149 AC: 22656 AN: 152182 Hom.: 2434 Cov.: 33 AF XY: 0.159 AC XY: 11863 AN XY: 74406

Gnomad4 AFR AF: 0.0636

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.149

Alfa AF: 0.130 Hom.: 868

Bravo AF: 0.147

Asia WGS AF: 0.381 AC: 1321 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Vascular endothelial growth factor (VEGF) inhibitor response Other:1

association, no assertion criteria provided

case-control

Department of Ophthalmology, College of Medicine, Hanyang University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.37
Dann	Benign	0.51

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: rs17081072; hg19: chr5-177747691;