Variant rs2395272 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001368882.1(COL13A1):c.463-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,603,484 control chromosomes in the GnomAD database, including 27,850 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3307 hom., cov: 32)

Exomes 𝑓: 0.16 ( 24543 hom. )

Consequence

COL13A1
NM_001368882.1 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00003695

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.704

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 10-69880499-G-A is Benign according to our data. Variant chr10-69880499-G-A is described in ClinVar as [Benign]. Clinvar id is 1217332.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL13A1	NM_001368882.1 linkuse as main transcript	c.463-4G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000645393.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL13A1	ENST00000645393.2 linkuse as main transcript	c.463-4G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			NM_001368882.1	P1

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29624

AN:

151806

Hom.:

3291

Cov.:

show subpopulations

Gnomad AFR

AF:

0.234

Gnomad AMI

AF:

0.0989

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.455

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.128

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.167

GnomAD3 exomes

AF:

0.219

AC:

53842

AN:

245334

Hom.:

7248

AF XY:

0.217

AC XY:

28948

AN XY:

133630

show subpopulations

Gnomad AFR exome

AF:

0.240

Gnomad AMR exome

AF:

0.310

Gnomad ASJ exome

AF:

0.133

Gnomad EAS exome

AF:

0.448

Gnomad SAS exome

AF:

0.316

Gnomad FIN exome

AF:

0.212

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.188

GnomAD4 exome

AF:

0.165

AC:

239223

AN:

1451562

Hom.:

24543

Cov.:

AF XY:

0.168

AC XY:

121714

AN XY:

722590

show subpopulations

Gnomad4 AFR exome

AF:

0.232

Gnomad4 AMR exome

AF:

0.299

Gnomad4 ASJ exome

AF:

0.137

Gnomad4 EAS exome

AF:

0.476

Gnomad4 SAS exome

AF:

0.308

Gnomad4 FIN exome

AF:

0.208

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.195

AC:

29661

AN:

151922

Hom.:

3307

Cov.:

AF XY:

0.201

AC XY:

14933

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.234

Gnomad4 AMR

AF:

0.233

Gnomad4 ASJ

AF:

0.143

Gnomad4 EAS

AF:

0.455

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.202

Gnomad4 NFE

AF:

0.139

Gnomad4 OTH

AF:

0.170

Alfa

AF:

0.143

Hom.:

1177

Bravo

AF:

0.199

Asia WGS

AF:

0.380

AC:

1319

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	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

-0.76

CADD

Benign

5.5

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000037

dbscSNV1_RF

Benign

0.0040

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