rs2236454

chr21-45473371-T-Cchr21-45473371-T-Gchr21-45473371-T-A

Variant summary

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

The NM_001379500.1(COL18A1):c.652-524T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,178 control chromosomes in the GnomAD database, including 21,283 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 0.50 (21283 hom., cov: 33)
• Consequence: COL18A1 NM_001379500.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

COL18A1 (HGNC:2195): (collagen type XVIII alpha 1 chain) This gene encodes the alpha chain of type XVIII collagen. This collagen is one of the multiplexins, extracellular matrix proteins that contain multiple triple-helix domains (collagenous domains) interrupted by non-collagenous domains. A long isoform of the protein has an N-terminal domain that is homologous to the extracellular part of frizzled receptors. Proteolytic processing at several endogenous cleavage sites in the C-terminal domain results in production of endostatin, a potent antiangiogenic protein that is able to inhibit angiogenesis and tumor growth. Mutations in this gene are associated with Knobloch syndrome. The main features of this syndrome involve retinal abnormalities, so type XVIII collagen may play an important role in retinal structure and in neural tube closure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL18A1	NM_001379500.1	c.652-524T>C		intron_variant		ENST00000651438.1
COL18A1	NM_030582.4	c.1192-524T>C		intron_variant
COL18A1	NM_130444.3	c.1897-524T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL18A1	ENST00000651438.1	c.652-524T>C		intron_variant			NM_001379500.1
COL18A1	ENST00000355480.10	c.1192-524T>C		intron_variant		1
COL18A1	ENST00000359759.8	c.1897-524T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76177 AN: 152058 Hom.: 21245 Cov.: 33

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.501 AC: 76266 AN: 152178 Hom.: 21283 Cov.: 33 AF XY: 0.497 AC XY: 36998 AN XY: 74384

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.489

Alfa AF: 0.431 Hom.: 3084

Bravo AF: 0.521

Asia WGS AF: 0.461 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.17
Dann	Benign	0.24

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: rs2236454; hg19: chr21-46893285;