5-178463054-G-A

Position:

• chr5-178463054-G-A

Variant summary

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

The NM_173465.4(COL23A1):​c.361+97628C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,182 control chromosomes in the GnomAD database, including 14,120 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 0.42 (14120 hom., cov: 34)
• Consequence: COL23A1 NM_173465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

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]

LOC124901148 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL23A1	NM_173465.4	c.361+97628C>T		intron_variant		ENST00000390654.8	NP_775736.2
LOC124901148	XR_007059080.1	n.9787C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL23A1	ENST00000390654.8	c.361+97628C>T		intron_variant		5	NM_173465.4	ENSP00000375069	P1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63254 AN: 152062 Hom.: 14113 Cov.: 34

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.416 AC: 63277 AN: 152182 Hom.: 14120 Cov.: 34 AF XY: 0.414 AC XY: 30803 AN XY: 74392

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.421

Alfa AF: 0.466 Hom.: 2933

Bravo AF: 0.423

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.70

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: rs9332465; hg19: chr5-177890055; COSMIC: COSV66787997;