10-69823442-C-T

Position:

• chr10-69823442-C-T

Variant summary

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

The NM_001368882.1(COL13A1):​c.364+1004C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,970 control chromosomes in the GnomAD database, including 10,393 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 (10393 hom., cov: 32)
• Consequence: COL13A1 NM_001368882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL13A1	NM_001368882.1	c.364+1004C>T		intron_variant		ENST00000645393.2	NP_001355811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL13A1	ENST00000645393.2	c.364+1004C>T		intron_variant			NM_001368882.1	ENSP00000496051	P1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54929 AN: 151854 Hom.: 10359 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.362 AC: 55013 AN: 151970 Hom.: 10393 Cov.: 32 AF XY: 0.361 AC XY: 26781 AN XY: 74254

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.374

Alfa AF: 0.327 Hom.: 17666

Bravo AF: 0.379

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.50

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: rs7077164; hg19: chr10-71583198;