chr5-178238341-G-A

Variant names:

• chr5-178238341-G-A
• rs1544926
• NM_173465.4:c.*357C>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.*357C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 233,896 control chromosomes in the GnomAD database, including 19,275 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 0.36 (11517 hom., cov: 33)
  • Exomes 𝑓: 0.42 (7758 hom.)
• Consequence: COL23A1 NM_173465.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 11 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]

LOC112267937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL23A1	NM_173465.4	c.*357C>T		3_prime_UTR_variant	Exon 29 of 29	ENST00000390654.8	NP_775736.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL23A1	ENST00000390654.8	c.*357C>T		3_prime_UTR_variant	Exon 29 of 29	5	NM_173465.4	ENSP00000375069.3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54893 AN: 152012 Hom.: 11521 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.416 AC: 34024 AN: 81766 Hom.: 7758 Cov.: 0 AF XY: 0.425 AC XY: 18551 AN XY: 43674

African (AFR) AF: 0.134 AC: 351 AN: 2624

American (AMR) AF: 0.424 AC: 1665 AN: 3928

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1343 AN: 2660

East Asian (EAS) AF: 0.182 AC: 1031 AN: 5672

South Asian (SAS) AF: 0.489 AC: 4157 AN: 8496

European-Finnish (FIN) AF: 0.409 AC: 1377 AN: 3366

Middle Eastern (MID) AF: 0.487 AC: 185 AN: 380

European-Non Finnish (NFE) AF: 0.441 AC: 22055 AN: 50056

Other (OTH) AF: 0.406 AC: 1860 AN: 4584

GnomAD4 genome AF: 0.361 AC: 54892 AN: 152130 Hom.: 11517 Cov.: 33 AF XY: 0.363 AC XY: 26966 AN XY: 74366

African (AFR) AF: 0.147 AC: 6112 AN: 41534

American (AMR) AF: 0.428 AC: 6531 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3472

East Asian (EAS) AF: 0.172 AC: 890 AN: 5162

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4820

European-Finnish (FIN) AF: 0.435 AC: 4606 AN: 10584

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31292 AN: 67968

Other (OTH) AF: 0.379 AC: 800 AN: 2112

Alfa AF: 0.426 Hom.: 39542

Bravo AF: 0.348

Asia WGS AF: 0.320 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.73
PhyloP100		-0.25
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: rs1544926; hg19: chr5-177665342; COSMIC: COSV66791335;