rs1544926

Positions:

• chr5-178238341-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.*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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
COL23A1	NM_173465.4	c.*357C>T		3_prime_UTR_variant	29/29	ENST00000390654.8
LOC112267937	XR_002956237.2	n.3087G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL23A1	ENST00000390654.8	c.*357C>T		3_prime_UTR_variant	29/29	5	NM_173465.4	P1

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

Gnomad4 AFR exome AF: 0.134

Gnomad4 AMR exome AF: 0.424

Gnomad4 ASJ exome AF: 0.505

Gnomad4 EAS exome AF: 0.182

Gnomad4 SAS exome AF: 0.489

Gnomad4 FIN exome AF: 0.409

Gnomad4 NFE exome AF: 0.441

Gnomad4 OTH exome AF: 0.406

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

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.379

Alfa AF: 0.453 Hom.: 25358

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

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: rs1544926; hg19: chr5-177665342; COSMIC: COSV66791335;