5-178346699-C-T

Variant names:

• chr5-178346699-C-T
• rs17641413
• NM_173465.4:c.362-39780G>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.362-39780G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,124 control chromosomes in the GnomAD database, including 9,888 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 0.34 (9888 hom., cov: 32)
• Consequence: COL23A1 NM_173465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 1 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=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173465.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL23A1	NM_173465.4	MANE Select	c.362-39780G>A		intron	N/A	NP_775736.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL23A1	ENST00000390654.8	TSL:5 MANE Select	c.362-39780G>A		intron	N/A	ENSP00000375069.3
	COL23A1	ENST00000407622.3	TSL:5	c.-69-39780G>A		intron	N/A	ENSP00000385092.3
	COL23A1	ENST00000679896.1		n.-69-39780G>A		intron	N/A	ENSP00000505024.1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51120 AN: 152006 Hom.: 9883 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.336 AC: 51138 AN: 152124 Hom.: 9888 Cov.: 32 AF XY: 0.335 AC XY: 24904 AN XY: 74362

African (AFR) AF: 0.158 AC: 6537 AN: 41490

American (AMR) AF: 0.368 AC: 5626 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3466

East Asian (EAS) AF: 0.103 AC: 533 AN: 5188

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4824

European-Finnish (FIN) AF: 0.416 AC: 4399 AN: 10566

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29690 AN: 67978

Other (OTH) AF: 0.393 AC: 829 AN: 2112

Alfa AF: 0.413 Hom.: 25288

Bravo AF: 0.325

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		1.3
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: rs17641413; hg19: chr5-177773700;