Genetic Variant COL6A2:p.Gly699Gly (chr21-46125912-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

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

The NM_001849.4(COL6A2):c.2097C>T(p.Gly699Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,612,538 control chromosomes in the GnomAD database, including 193,839 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 16252 hom., cov: 31)

Exomes 𝑓: 0.49 ( 177587 hom. )

Consequence

COL6A2
NM_001849.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:15

Conservation

PhyloP100: -1.67

Publications

22 publications found

Variant links:

Genes affected

COL6A2 (HGNC:2212): (collagen type VI alpha 2 chain) This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand Factor type A domains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in this gene are associated with Bethlem myopathy and Ullrich scleroatonic muscular dystrophy. Three transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]

COL6A2 Gene-Disease associations (from GenCC):

collagen 6-related myopathy
Inheritance: AD, SD, AR Classification: DEFINITIVE Submitted by: ClinGen
Ullrich congenital muscular dystrophy 1B
Inheritance: AR, AD Classification: DEFINITIVE Submitted by: G2P
Bethlem myopathy 1A
Inheritance: AD, AR Classification: STRONG Submitted by: Genomics England PanelApp
Ullrich congenital muscular dystrophy 1A
Inheritance: AR, AD Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
Bethlem myopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Ullrich congenital muscular dystrophy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
myosclerosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

COL6A2 links:

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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=-0.61).

BP6

Variant 21-46125912-C-T is Benign according to our data. Variant chr21-46125912-C-T is described in ClinVar as Benign. ClinVar VariationId is 93931.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.67 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001849.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
COL6A2	NM_001849.4	MANE Select	c.2097C>T	p.Gly699Gly	synonymous	Exon 26 of 28	NP_001840.3
COL6A2	NM_058174.3	MANE Plus Clinical	c.2097C>T	p.Gly699Gly	synonymous	Exon 26 of 28	NP_478054.2	P12110-2
COL6A2	NM_058175.3		c.2097C>T	p.Gly699Gly	synonymous	Exon 26 of 28	NP_478055.2	P12110-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
COL6A2	ENST00000300527.9	TSL:1 MANE Select	c.2097C>T	p.Gly699Gly	synonymous	Exon 26 of 28	ENSP00000300527.4	P12110-1
COL6A2	ENST00000397763.6	TSL:5 MANE Plus Clinical	c.2097C>T	p.Gly699Gly	synonymous	Exon 26 of 28	ENSP00000380870.1	P12110-2
COL6A2	ENST00000857098.1		c.2292C>T	p.Gly764Gly	synonymous	Exon 26 of 28	ENSP00000527157.1

Frequencies

GnomAD3 genomes

AF:

0.444

AC:

67395

AN:

151666

Hom.:

16237

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.581

Gnomad AMR

AF:

0.576

Gnomad ASJ

AF:

0.524

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.615

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.460

GnomAD2 exomes

AF:

0.491

AC:

123074

AN:

250738

AF XY:

0.481

show subpopulations

Gnomad AFR exome

AF:

0.241

Gnomad AMR exome

AF:

0.653

Gnomad ASJ exome

AF:

0.519

Gnomad EAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.620

Gnomad NFE exome

AF:

0.501

Gnomad OTH exome

AF:

0.516

GnomAD4 exome

AF:

0.487

AC:

711780

AN:

1460752

Hom.:

177587

Cov.:

AF XY:

0.483

AC XY:

350674

AN XY:

726700

show subpopulations

African (AFR)

AF:

0.229

AC:

7662

AN:

33478

American (AMR)

AF:

0.644

AC:

28798

AN:

44702

Ashkenazi Jewish (ASJ)

AF:

0.521

AC:

13606

AN:

26132

East Asian (EAS)

AF:

0.433

AC:

17167

AN:

39692

South Asian (SAS)

AF:

0.331

AC:

28559

AN:

86254

European-Finnish (FIN)

AF:

0.612

AC:

32142

AN:

52532

Middle Eastern (MID)

AF:

0.431

AC:

2485

AN:

5766

European-Non Finnish (NFE)

AF:

0.497

AC:

552578

AN:

1111818

Other (OTH)

AF:

0.477

AC:

28783

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.439

Heterozygous variant carriers

23227

46454

69681

92908

116135

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15966

31932

47898

63864

79830

<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:

0.444

AC:

67427

AN:

151786

Hom.:

16252

Cov.:

AF XY:

0.450

AC XY:

33321

AN XY:

74114

show subpopulations

African (AFR)

AF:

0.250

AC:

10337

AN:

41416

American (AMR)

AF:

0.576

AC:

8803

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.524

AC:

1815

AN:

3466

East Asian (EAS)

AF:

0.450

AC:

2294

AN:

5102

South Asian (SAS)

AF:

0.332

AC:

1596

AN:

4804

European-Finnish (FIN)

AF:

0.615

AC:

6476

AN:

10534

Middle Eastern (MID)

AF:

0.425

AC:

124

AN:

292

European-Non Finnish (NFE)

AF:

0.508

AC:

34493

AN:

67878

Other (OTH)

AF:

0.455

AC:

960

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1851

3702

5553

7404

9255

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

610

1220

1830

2440

3050

<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:

0.470

Hom.:

7593

Bravo

AF:

0.436

Asia WGS

AF:

0.401

AC:

1394

AN:

3478

EpiCase

AF:

0.492

EpiControl

AF:

0.489

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (6)

not provided (3)

Bethlem myopathy 1A (2)

Myosclerosis (2)

Collagen 6-related myopathy (1)

Ullrich congenital muscular dystrophy 1A (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

2.8

(source)

DANN

Benign

0.91

PhyloP100

-1.7

Mutation Taster

=95/5

polymorphism (auto)

(source)

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

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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