NM_000393.5:c.2498C>T

Variant names:

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP3BP6_Very_StrongBS1BS2

The NM_000393.5(COL5A2):c.2498C>T(p.Pro833Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 1,613,182 control chromosomes in the GnomAD database, including 426 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 23 hom., cov: 32)

Exomes 𝑓: 0.021 ( 403 hom. )

Consequence

COL5A2
NM_000393.5 missense, splice_region

Scores

Splicing: ADA: 0.9930

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:14

Conservation

PhyloP100: 7.78

Variant links:

Genes affected

COL5A2 (HGNC:2210): (collagen type V alpha 2 chain) This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. [provided by RefSeq, Jul 2008]

COL5A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

PP3

Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.

BP6

Variant 2-189053896-G-A is Benign according to our data. Variant chr2-189053896-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 136944.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-189053896-G-A is described in Lovd as [Benign]. Variant chr2-189053896-G-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0153 (2329/152240) while in subpopulation NFE AF= 0.02 (1359/68010). AF 95% confidence interval is 0.0191. There are 23 homozygotes in gnomad4. There are 1144 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2329 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL5A2	NM_000393.5 link	c.2498C>T	p.Pro833Leu	missense_variant, splice_region_variant	Exon 37 of 54	ENST00000374866.9	NP_000384.2	P05997
COL5A2	XM_011510573.4 link	c.2360C>T	p.Pro787Leu	missense_variant, splice_region_variant	Exon 40 of 57		XP_011508875.1
COL5A2	XM_047443251.1 link	c.2360C>T	p.Pro787Leu	missense_variant, splice_region_variant	Exon 42 of 59		XP_047299207.1
COL5A2	XM_047443252.1 link	c.2360C>T	p.Pro787Leu	missense_variant, splice_region_variant	Exon 41 of 58		XP_047299208.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL5A2	ENST00000374866.9 link	c.2498C>T	p.Pro833Leu	missense_variant, splice_region_variant	Exon 37 of 54	1	NM_000393.5	ENSP00000364000.3		P05997
COL5A2	ENST00000618828.1 link	c.1337C>T	p.Pro446Leu	missense_variant, splice_region_variant	Exon 30 of 47	5		ENSP00000482184.1		A0A087WYX9

Frequencies

GnomAD3 genomes

AF:

0.0153

AC:

2332

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00374

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0118

Gnomad ASJ

AF:

0.0233

Gnomad EAS

AF:

0.00251

Gnomad SAS

AF:

0.0131

Gnomad FIN

AF:

0.0324

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0200

Gnomad OTH

AF:

0.0182

GnomAD3 exomes

AF:

0.0170

AC:

4270

AN:

250982

Hom.:

AF XY:

0.0176

AC XY:

2384

AN XY:

135688

show subpopulations

Gnomad AFR exome

AF:

0.00371

Gnomad AMR exome

AF:

0.00996

Gnomad ASJ exome

AF:

0.0263

Gnomad EAS exome

AF:

0.000327

Gnomad SAS exome

AF:

0.0125

Gnomad FIN exome

AF:

0.0325

Gnomad NFE exome

AF:

0.0212

Gnomad OTH exome

AF:

0.0170

GnomAD4 exome

AF:

0.0209

AC:

30601

AN:

1460942

Hom.:

403

Cov.:

AF XY:

0.0208

AC XY:

15118

AN XY:

726856

show subpopulations

Gnomad4 AFR exome

AF:

0.00302

Gnomad4 AMR exome

AF:

0.0113

Gnomad4 ASJ exome

AF:

0.0278

Gnomad4 EAS exome

AF:

0.00385

Gnomad4 SAS exome

AF:

0.0135

Gnomad4 FIN exome

AF:

0.0299

Gnomad4 NFE exome

AF:

0.0226

Gnomad4 OTH exome

AF:

0.0187

GnomAD4 genome

AF:

0.0153

AC:

2329

AN:

152240

Hom.:

Cov.:

AF XY:

0.0154

AC XY:

1144

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00373

Gnomad4 AMR

AF:

0.0117

Gnomad4 ASJ

AF:

0.0233

Gnomad4 EAS

AF:

0.00251

Gnomad4 SAS

AF:

0.0129

Gnomad4 FIN

AF:

0.0324

Gnomad4 NFE

AF:

0.0200

Gnomad4 OTH

AF:

0.0180

Alfa

AF:

0.0197

Hom.:

Bravo

AF:

0.0142

TwinsUK

AF:

0.0237

AC:

ALSPAC

AF:

0.0280

AC:

108

ESP6500AA

AF:

0.00454

AC:

ESP6500EA

AF:

0.0209

AC:

180

ExAC

AF:

0.0170

AC:

2063

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.0220

EpiControl

AF:

0.0201

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:14

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 11, 2012

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Jul 21, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:3

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

COL5A2: PP2, BS1, BS2 -

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Ehlers-Danlos syndrome, classic type, 2

Benign:2

Nov 27, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Familial thoracic aortic aneurysm and aortic dissection

Benign:1

Mar 03, 2015

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Ehlers-Danlos syndrome type 7A

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Ehlers-Danlos syndrome

Benign:1

Jul 16, 2022

Genome Diagnostics Laboratory, The Hospital for Sick Children

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Ehlers-Danlos syndrome, classic type

Benign:1

Jun 15, 2023

Molecular Genetics, Royal Melbourne Hospital

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Ehlers-Danlos syndrome, classic type, 1

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.16

BayesDel_noAF

Uncertain

0.020

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.83

D;T;D

Eigen

Pathogenic

0.86

Eigen_PC

Pathogenic

0.85

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.92

.;D;D

MetaRNN

Benign

0.014

T;T;T

MetaSVM

Uncertain

0.71

MutationAssessor

Uncertain

2.5

M;.;M

PrimateAI

Uncertain

0.78

PROVEAN

Pathogenic

-7.5

D;.;.

REVEL

Uncertain

0.60

Sift

Pathogenic

0.0

D;.;.

Sift4G

Uncertain

0.0020

D;D;.

Polyphen

0.98

D;.;D

Vest4

0.61

MPC

0.26

ClinPred

0.027

GERP RS

5.9

Varity_R

0.67

gMVP

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

0.99

dbscSNV1_RF

Pathogenic

0.84

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