rs3858158

chr10-69880294-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001368882.1(COL13A1):c.463-209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 151,210 control chromosomes in the GnomAD database, including 3,109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (3109 hom., cov: 32)
• Consequence: COL13A1 NM_001368882.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.312

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 10-69880294-T-C is Benign according to our data. Variant chr10-69880294-T-C is described in ClinVar as [Benign]. Clinvar id is 1278613.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL13A1	NM_001368882.1	c.463-209T>C		intron_variant		ENST00000645393.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL13A1	ENST00000645393.2	c.463-209T>C		intron_variant			NM_001368882.1	P1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26508 AN: 151090 Hom.: 3092 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.0268

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.0765

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.176 AC: 26550 AN: 151210 Hom.: 3109 Cov.: 32 AF XY: 0.179 AC XY: 13201 AN XY: 73930

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.0765

Gnomad4 NFE AF: 0.0997

Gnomad4 OTH AF: 0.167

Alfa AF: 0.134 Hom.: 279

Bravo AF: 0.189

Asia WGS AF: 0.390 AC: 1354 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.0
Dann	Benign	0.69

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: rs3858158; hg19: chr10-71640050;