7-94401587-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000089.4(COL1A2):c.246T>C(p.Asp82Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,560,246 control chromosomes in the GnomAD database, including 24,919 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 6961 hom., cov: 30)

Exomes 𝑓: 0.14 ( 17958 hom. )

Consequence

COL1A2
NM_000089.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 1.38

Publications

37 publications found

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 Gene-Disease associations (from GenCC):

Ehlers-Danlos syndrome, arthrochalasia type, 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Illumina, PanelApp Australia, Labcorp Genetics (formerly Invitae)
osteogenesis imperfecta
Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
osteogenesis imperfecta type 1
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
osteogenesis imperfecta type 2
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen
osteogenesis imperfecta type 3
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
osteogenesis imperfecta type 4
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
Ehlers-Danlos syndrome, arthrochalasia type
Inheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
Ehlers-Danlos syndrome, cardiac valvular type
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, ClinGen, PanelApp Australia, Orphanet, G2P
combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2
Inheritance: AD Classification: MODERATE Submitted by: ClinGen, Ambry Genetics
Ehlers-Danlos/osteogenesis imperfecta syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
high bone mass osteogenesis imperfecta
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

COL1A2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 7-94401587-T-C is Benign according to our data. Variant chr7-94401587-T-C is described in ClinVar as Benign. ClinVar VariationId is 254955.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.38 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000089.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL1A2	NM_000089.4	MANE Select	c.246T>C	p.Asp82Asp	synonymous	Exon 6 of 52	NP_000080.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
COL1A2	ENST00000297268.11	TSL:1 MANE Select	c.246T>C	p.Asp82Asp	synonymous	Exon 6 of 52	ENSP00000297268.6
COL1A2	ENST00000959377.1		c.246T>C	p.Asp82Asp	synonymous	Exon 6 of 52	ENSP00000629436.1
COL1A2	ENST00000959379.1		c.246T>C	p.Asp82Asp	synonymous	Exon 6 of 52	ENSP00000629438.1

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

36909

AN:

150588

Hom.:

6937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.516

Gnomad AMI

AF:

0.100

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.405

Gnomad SAS

AF:

0.0980

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.236

GnomAD2 exomes

AF:

0.165

AC:

40326

AN:

245108

AF XY:

0.153

show subpopulations

Gnomad AFR exome

AF:

0.525

Gnomad AMR exome

AF:

0.133

Gnomad ASJ exome

AF:

0.149

Gnomad EAS exome

AF:

0.390

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.154

GnomAD4 exome

AF:

0.137

AC:

193444

AN:

1409550

Hom.:

17958

Cov.:

AF XY:

0.134

AC XY:

94138

AN XY:

700838

show subpopulations

African (AFR)

AF:

0.522

AC:

16721

AN:

32014

American (AMR)

AF:

0.138

AC:

5895

AN:

42756

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

3581

AN:

24680

East Asian (EAS)

AF:

0.426

AC:

15976

AN:

37524

South Asian (SAS)

AF:

0.0842

AC:

6581

AN:

78198

European-Finnish (FIN)

AF:

0.111

AC:

5528

AN:

49722

Middle Eastern (MID)

AF:

0.171

AC:

763

AN:

4456

European-Non Finnish (NFE)

AF:

0.119

AC:

129082

AN:

1082816

Other (OTH)

AF:

0.162

AC:

9317

AN:

57384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

6661

13322

19983

26644

33305

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5010

10020

15030

20040

25050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.245

AC:

36975

AN:

150696

Hom.:

6961

Cov.:

AF XY:

0.242

AC XY:

17812

AN XY:

73636

show subpopulations

African (AFR)

AF:

0.516

AC:

21225

AN:

41098

American (AMR)

AF:

0.176

AC:

2672

AN:

15170

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

541

AN:

3466

East Asian (EAS)

AF:

0.404

AC:

2075

AN:

5130

South Asian (SAS)

AF:

0.0985

AC:

473

AN:

4804

European-Finnish (FIN)

AF:

0.105

AC:

1052

AN:

10060

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8289

AN:

67676

Other (OTH)

AF:

0.239

AC:

498

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1121

2242

3363

4484

5605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.159

Hom.:

4614

Bravo

AF:

0.267

Asia WGS

AF:

0.292

AC:

1010

AN:

3462

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (4)

Cardiovascular phenotype (1)

Ehlers-Danlos syndrome, arthrochalasia type, 2 (1)

not provided (1)

Osteogenesis imperfecta (1)

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

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.48

PhyloP100

1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

Splicevardb

2.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over