NM_000089.4:c.1878G>T

Variant names:

Variant summary

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

The NM_000089.4(COL1A2):c.1878G>T(p.Val626Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0246 in 1,595,068 control chromosomes in the GnomAD database, including 3,447 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.032 ( 435 hom., cov: 32)

Exomes 𝑓: 0.024 ( 3012 hom. )

Consequence

COL1A2
NM_000089.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.290

Variant links:

Genes affected

COL1A2 (HGNC:2198): (collagen type I alpha 2 chain) This gene encodes the pro-alpha2 chain of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIB, recessive Ehlers-Danlos syndrome Classical type, idiopathic osteoporosis, and atypical Marfan syndrome. Symptoms associated with mutations in this gene, however, tend to be less severe than mutations in the gene for the alpha1 chain of type I collagen (COL1A1) reflecting the different role of alpha2 chains in matrix integrity. Three transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]

COL1A2 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=-0.85).

BP6

Variant 7-94417738-G-T is Benign according to our data. Variant chr7-94417738-G-T is described in ClinVar as [Benign]. Clinvar id is 360958.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-94417738-G-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.29 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL1A2	NM_000089.4 link	c.1878G>T	p.Val626Val	synonymous_variant	Exon 32 of 52	ENST00000297268.11	NP_000080.2	P08123A0A0S2Z3H5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
COL1A2	ENST00000297268.11 link	c.1878G>T	p.Val626Val	synonymous_variant	Exon 32 of 52	1	NM_000089.4	ENSP00000297268.6	P08123
COL1A2	ENST00000473573.5 link	n.215G>T		non_coding_transcript_exon_variant	Exon 4 of 11	2
COL1A2	ENST00000497316.5 link	n.275G>T		non_coding_transcript_exon_variant	Exon 1 of 9	2
COL1A2	ENST00000461525.5 link	n.-34G>T		upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0317

AC:

4827

AN:

152102

Hom.:

434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0184

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0471

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.375

Gnomad SAS

AF:

0.0663

Gnomad FIN

AF:

0.0322

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00935

Gnomad OTH

AF:

0.0330

GnomAD3 exomes

AF:

0.0520

AC:

11443

AN:

219926

Hom.:

1209

AF XY:

0.0494

AC XY:

5805

AN XY:

117588

show subpopulations

Gnomad AFR exome

AF:

0.0175

Gnomad AMR exome

AF:

0.0664

Gnomad ASJ exome

AF:

0.0106

Gnomad EAS exome

AF:

0.363

Gnomad SAS exome

AF:

0.0530

Gnomad FIN exome

AF:

0.0318

Gnomad NFE exome

AF:

0.00890

Gnomad OTH exome

AF:

0.0346

GnomAD4 exome

AF:

0.0239

AC:

34438

AN:

1442848

Hom.:

3012

Cov.:

AF XY:

0.0243

AC XY:

17376

AN XY:

715382

show subpopulations

Gnomad4 AFR exome

AF:

0.0158

Gnomad4 AMR exome

AF:

0.0607

Gnomad4 ASJ exome

AF:

0.0100

Gnomad4 EAS exome

AF:

0.357

Gnomad4 SAS exome

AF:

0.0534

Gnomad4 FIN exome

AF:

0.0316

Gnomad4 NFE exome

AF:

0.00809

Gnomad4 OTH exome

AF:

0.0357

GnomAD4 genome

AF:

0.0318

AC:

4836

AN:

152220

Hom.:

435

Cov.:

AF XY:

0.0357

AC XY:

2660

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0185

Gnomad4 AMR

AF:

0.0472

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.374

Gnomad4 SAS

AF:

0.0662

Gnomad4 FIN

AF:

0.0322

Gnomad4 NFE

AF:

0.00934

Gnomad4 OTH

AF:

0.0378

Alfa

AF:

0.0131

Hom.:

Bravo

AF:

0.0345

Asia WGS

AF:

0.226

AC:

785

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Oct 20, 2016

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 28, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Osteogenesis imperfecta

Benign:1

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. -

Ehlers-danlos syndrome, arthrochalasia type, 2

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Osteogenesis imperfecta type I;C0268335:Ehlers-Danlos syndrome, classic type, 1

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype

Benign:1

Jan 04, 2019

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.8

DANN

Benign

0.51

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