5-178463054-G-A

Variant names:

• chr5-178463054-G-A
• rs9332465
• NM_173465.4:c.361+97628C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

LOC124901148 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
COL23A1	NM_173465.4	c.361+97628C>T		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.361+97628C>T		intron_variant	Intron 2 of 28	5	NM_173465.4	ENSP00000375069.3

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

African (AFR) AF: 0.267 AC: 11101 AN: 41508

American (AMR) AF: 0.560 AC: 8556 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5172

South Asian (SAS) AF: 0.295 AC: 1425 AN: 4832

European-Finnish (FIN) AF: 0.445 AC: 4710 AN: 10590

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32814 AN: 68004

Other (OTH) AF: 0.421 AC: 889 AN: 2112

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
PhyloP100		1.7
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: rs9332465; hg19: chr5-177890055; COSMIC: COSV66787997;