rs10823435

chr10-69819925-G-Achr10-69819925-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.295-2444G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,144 control chromosomes in the GnomAD database, including 10,280 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 0.34 (10280 hom., cov: 32)
• Consequence: COL13A1 NM_001368882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL13A1	NM_001368882.1	c.295-2444G>A		intron_variant		ENST00000645393.2
LOC105378347	XR_946039.3	n.127+876C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL13A1	ENST00000645393.2	c.295-2444G>A		intron_variant			NM_001368882.1	P1
	ENST00000690087.2	n.134+876C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52362 AN: 152026 Hom.: 10281 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.344 AC: 52373 AN: 152144 Hom.: 10280 Cov.: 32 AF XY: 0.345 AC XY: 25647 AN XY: 74384

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.381

Alfa AF: 0.381 Hom.: 1783

Bravo AF: 0.341

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.30
Dann	Benign	0.67

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: rs10823435; hg19: chr10-71579681;