rs2763341

Variant names:

• chr10-69822699-G-A
• rs2763341
• NM_001368882.1:c.364+261G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-69822699-G-A
• chr10-69822699-G-C
• chr10-69822699-G-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001368882.1(COL13A1):​c.364+261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,202 control chromosomes in the GnomAD database, including 48,388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.80 (48388 hom., cov: 33)
• Consequence: COL13A1 NM_001368882.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.361
• Publications: 6 publications found

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 Gene-Disease associations (from GenCC):

• congenital myasthenic syndrome 19

  Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• presynaptic congenital myasthenic syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• postsynaptic congenital myasthenic syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 10-69822699-G-A is Benign according to our data. Variant chr10-69822699-G-A is described in ClinVar as [Benign]. Clinvar id is 1245398.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL13A1	NM_001368882.1	c.364+261G>A		intron_variant	Intron 2 of 40	ENST00000645393.2	NP_001355811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL13A1	ENST00000645393.2	c.364+261G>A		intron_variant	Intron 2 of 40		NM_001368882.1	ENSP00000496051.1

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121093 AN: 152084 Hom.: 48353 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.796 AC: 121183 AN: 152202 Hom.: 48388 Cov.: 33 AF XY: 0.796 AC XY: 59215 AN XY: 74424

African (AFR) AF: 0.733 AC: 30434 AN: 41508

American (AMR) AF: 0.720 AC: 11000 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4365 AN: 5174

South Asian (SAS) AF: 0.893 AC: 4309 AN: 4824

European-Finnish (FIN) AF: 0.845 AC: 8965 AN: 10604

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56386 AN: 68012

Other (OTH) AF: 0.785 AC: 1662 AN: 2116

Alfa AF: 0.820 Hom.: 218516

Bravo AF: 0.785

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.73
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2763341; hg19: chr10-71582455;