chr5-178381674-C-T

Position:

• chr5-178381674-C-T

Variant summary

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

The NM_173465.4(COL23A1):​c.362-74755G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,028 control chromosomes in the GnomAD database, including 3,915 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 0.21 (3915 hom., cov: 32)
• Consequence: COL23A1 NM_173465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL23A1	NM_173465.4	c.362-74755G>A		intron_variant		ENST00000390654.8	NP_775736.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL23A1	ENST00000390654.8	c.362-74755G>A		intron_variant		5	NM_173465.4	ENSP00000375069.3

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31759 AN: 151910 Hom.: 3903 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.209 AC: 31818 AN: 152028 Hom.: 3915 Cov.: 32 AF XY: 0.213 AC XY: 15814 AN XY: 74286

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.202

Alfa AF: 0.181 Hom.: 355

Bravo AF: 0.215

Asia WGS AF: 0.320 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.41

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: rs2910124; hg19: chr5-177808675;