rs2683572

Positions:

• chr10-69889553-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001368882.1(COL13A1):​c.603+113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 1,375,432 control chromosomes in the GnomAD database, including 456,439 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.79 (48399 hom., cov: 33)
  • Exomes 𝑓: 0.81 (408040 hom.)
• Consequence: COL13A1 NM_001368882.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -4.28

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]

COL13A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 10-69889553-A-G is Benign according to our data. Variant chr10-69889553-A-G is described in ClinVar as [Benign]. Clinvar id is 1274483.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL13A1	NM_001368882.1	c.603+113A>G		intron_variant		ENST00000645393.2	NP_001355811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL13A1	ENST00000645393.2	c.603+113A>G		intron_variant			NM_001368882.1	ENSP00000496051.1

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120877 AN: 152086 Hom.: 48372 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.826

GnomAD4 exome AF: 0.814 AC: 995191 AN: 1223228 Hom.: 408040 AF XY: 0.812 AC XY: 496531 AN XY: 611724

Gnomad4 AFR exome AF: 0.773

Gnomad4 AMR exome AF: 0.642

Gnomad4 ASJ exome AF: 0.851

Gnomad4 EAS exome AF: 0.543

Gnomad4 SAS exome AF: 0.715

Gnomad4 FIN exome AF: 0.845

Gnomad4 NFE exome AF: 0.837

Gnomad4 OTH exome AF: 0.806

GnomAD4 genome AF: 0.795 AC: 120951 AN: 152204 Hom.: 48399 Cov.: 33 AF XY: 0.791 AC XY: 58869 AN XY: 74410

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.822

Alfa AF: 0.806 Hom.: 19142

Bravo AF: 0.784

Asia WGS AF: 0.624 AC: 2171 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.75

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: rs2683572; hg19: chr10-71649309; COSMIC: COSV62570801;