rs1227756

chr10-69828748-G-Achr10-69828748-G-C

Variant summary

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

The NM_001368882.1(COL13A1):c.364+6310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,016 control chromosomes in the GnomAD database, including 17,141 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 0.47 (17141 hom., cov: 33)
• Consequence: COL13A1 NM_001368882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL13A1	NM_001368882.1	c.364+6310G>A		intron_variant		ENST00000645393.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL13A1	ENST00000645393.2	c.364+6310G>A		intron_variant			NM_001368882.1	P1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70968 AN: 151898 Hom.: 17134 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.467 AC: 70980 AN: 152016 Hom.: 17141 Cov.: 33 AF XY: 0.460 AC XY: 34163 AN XY: 74298

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.455

Alfa AF: 0.523 Hom.: 47554

Bravo AF: 0.456

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.2
Dann	Benign	0.84

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: rs1227756; hg19: chr10-71588504;