5-178413381-C-T

Variant names:

• chr5-178413381-C-T
• rs10070303
• NM_173465.4:c.362-106462G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173465.4(COL23A1):​c.362-106462G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,076 control chromosomes in the GnomAD database, including 5,189 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 0.23 (5189 hom., cov: 33)
• Consequence: COL23A1 NM_173465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL23A1	NM_173465.4	c.362-106462G>A		intron_variant	Intron 2 of 28	ENST00000390654.8	NP_775736.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL23A1	ENST00000390654.8	c.362-106462G>A		intron_variant	Intron 2 of 28	5	NM_173465.4	ENSP00000375069.3

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34395 AN: 151958 Hom.: 5166 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.227 AC: 34456 AN: 152076 Hom.: 5189 Cov.: 33 AF XY: 0.230 AC XY: 17130 AN XY: 74352

African (AFR) AF: 0.417 AC: 17297 AN: 41436

American (AMR) AF: 0.222 AC: 3387 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1986 AN: 5184

South Asian (SAS) AF: 0.230 AC: 1110 AN: 4824

European-Finnish (FIN) AF: 0.168 AC: 1774 AN: 10568

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7819 AN: 67992

Other (OTH) AF: 0.205 AC: 433 AN: 2116

Alfa AF: 0.165 Hom.: 6851

Bravo AF: 0.239

Asia WGS AF: 0.266 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10070303; hg19: chr5-177840382;