Variant rs11816811 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001368882.1(COL13A1):c.525A>C(p.Gly175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,611,854 control chromosomes in the GnomAD database, including 9,499 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 895 hom., cov: 31)

Exomes 𝑓: 0.11 ( 8604 hom. )

Consequence

COL13A1
NM_001368882.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.294

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 10-69887467-A-C is Benign according to our data. Variant chr10-69887467-A-C is described in ClinVar as [Benign]. Clinvar id is 1217334.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.294 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL13A1	NM_001368882.1 linkuse as main transcript	c.525A>C	p.Gly175=	synonymous_variant	8/41	ENST00000645393.2	NP_001355811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL13A1	ENST00000645393.2 linkuse as main transcript	c.525A>C	p.Gly175=	synonymous_variant	8/41		NM_001368882.1	ENSP00000496051	P1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16067

AN:

151202

Hom.:

896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0995

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.0897

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.0766

Gnomad SAS

AF:

0.0789

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.128

GnomAD3 exomes

AF:

0.100

AC:

24846

AN:

248540

Hom.:

1335

AF XY:

0.101

AC XY:

13569

AN XY:

134838

show subpopulations

Gnomad AFR exome

AF:

0.0944

Gnomad AMR exome

AF:

0.0548

Gnomad ASJ exome

AF:

0.197

Gnomad EAS exome

AF:

0.0894

Gnomad SAS exome

AF:

0.0748

Gnomad FIN exome

AF:

0.107

Gnomad NFE exome

AF:

0.112

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.106

AC:

154669

AN:

1460536

Hom.:

8604

Cov.:

AF XY:

0.106

AC XY:

76730

AN XY:

726584

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0576

Gnomad4 ASJ exome

AF:

0.199

Gnomad4 EAS exome

AF:

0.0651

Gnomad4 SAS exome

AF:

0.0750

Gnomad4 FIN exome

AF:

0.106

Gnomad4 NFE exome

AF:

0.109

Gnomad4 OTH exome

AF:

0.112

GnomAD4 genome

AF:

0.106

AC:

16068

AN:

151318

Hom.:

895

Cov.:

AF XY:

0.106

AC XY:

7791

AN XY:

73838

show subpopulations

Gnomad4 AFR

AF:

0.0994

Gnomad4 AMR

AF:

0.0896

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.0764

Gnomad4 SAS

AF:

0.0785

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.113

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.112

Hom.:

718

Bravo

AF:

0.104

Asia WGS

AF:

0.0770

AC:

267

AN:

3478

EpiCase

AF:

0.115

EpiControl

AF:

0.113

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Congenital myasthenic syndrome 19

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.73

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over