rs2637229

Positions:

• chr10-69929392-G-A
• chr10-69929392-G-C
• chr10-69929392-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001368882.1(COL13A1):​c.1485+393G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,530 control chromosomes in the GnomAD database, including 26,072 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 0.59 (26072 hom., cov: 29)
• Consequence: COL13A1 NM_001368882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

Genes affected

COL13A1 (HGNC:2190): (collagen type XIII alpha 1 chain) This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective tissues. Unlike most of the collagens, which are secreted into the extracellular matrix, collagen XIII contains a transmembrane domain and the protein has been localized to the plasma membrane. The transcripts for this gene undergo complex and extensive splicing involving at least eight exons. Like other collagens, collagen XIII is a trimer; it is not known whether this trimer is composed of one or more than one alpha chain isomer. A number of alternatively spliced transcript variants have been described, but the full length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL13A1	NM_001368882.1	c.1485+393G>A		intron_variant		ENST00000645393.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL13A1	ENST00000645393.2	c.1485+393G>A		intron_variant			NM_001368882.1	P1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88786 AN: 151412 Hom.: 26052 Cov.: 29

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.586 AC: 88832 AN: 151530 Hom.: 26072 Cov.: 29 AF XY: 0.587 AC XY: 43423 AN XY: 73996

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.590

Alfa AF: 0.561 Hom.: 47316

Bravo AF: 0.582

Asia WGS AF: 0.518 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.65

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: rs2637229; hg19: chr10-71689148;