10-69844853-A-G

Variant summary

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

The NM_001368882.1(COL13A1):c.364+22415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,224 control chromosomes in the GnomAD database, including 50,018 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 0.81 (50018 hom., cov: 34)
• Consequence: COL13A1 NM_001368882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL13A1	NM_001368882.1	c.364+22415A>G		intron_variant		ENST00000645393.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL13A1	ENST00000645393.2	c.364+22415A>G		intron_variant			NM_001368882.1	P1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122591 AN: 152106 Hom.: 49988 Cov.: 34

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.806 AC: 122675 AN: 152224 Hom.: 50018 Cov.: 34 AF XY: 0.810 AC XY: 60285 AN XY: 74430

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.936

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.812

Alfa AF: 0.814 Hom.: 7470

Bravo AF: 0.788

Asia WGS AF: 0.869 AC: 3022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.6
Dann	Benign	0.55

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: rs2704482; hg19: chr10-71604609;