GeneBe

rs4096395

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001368882.1(COL13A1):​c.2146-251C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

COL13A1
NM_001368882.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.168

Publications

0 publications found
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 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

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COL13A1NM_001368882.1 linkc.2146-251C>A intron_variant Intron 39 of 40 ENST00000645393.2 NP_001355811.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COL13A1ENST00000645393.2 linkc.2146-251C>A intron_variant Intron 39 of 40 NM_001368882.1 ENSP00000496051.1 A0A2R8YGI3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
273942
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
141988
African (AFR)
AF:
0.00
AC:
0
AN:
9708
American (AMR)
AF:
0.00
AC:
0
AN:
14750
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
8718
East Asian (EAS)
AF:
0.00
AC:
0
AN:
22282
South Asian (SAS)
AF:
0.00
AC:
0
AN:
21998
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
17278
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1250
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
161514
Other (OTH)
AF:
0.00
AC:
0
AN:
16444
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
5.4
DANN
Benign
0.54
PhyloP100
0.17

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

Other links and lift over

dbSNP: rs4096395; hg19: chr10-71716509; API