dbSNP rs10201909: COL6A3:p.Arg3043Arg (chr2-237334726-G-A) – 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_004369.4(COL6A3):c.9129C>T(p.Arg3043Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0261 in 1,613,994 control chromosomes in the GnomAD database, including 1,633 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.063 ( 695 hom., cov: 32)

Exomes 𝑓: 0.022 ( 938 hom. )

Consequence

COL6A3
NM_004369.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -2.59

Publications

8 publications found

Variant links:

Genes affected

COL6A3 (HGNC:2213): (collagen type VI alpha 3 chain) This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2 chains. This difference in size is largely due to an increase in the number of subdomains, similar to von Willebrand Factor type A domains, that are found in the amino terminal globular domain of all the alpha chains. 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 the type VI collagen genes are associated with Bethlem myopathy, a rare autosomal dominant proximal myopathy with early childhood onset. Mutations in this gene are also a cause of Ullrich congenital muscular dystrophy, also referred to as Ullrich scleroatonic muscular dystrophy, an autosomal recessive congenital myopathy that is more severe than Bethlem myopathy. Multiple transcript variants have been identified, but the full-length nature of only some of these variants has been described. [provided by RefSeq, Jun 2009]

COL6A3 Gene-Disease associations (from GenCC):

Bethlem myopathy 1A
Inheritance: AD, AR, SD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Ambry Genetics
collagen 6-related myopathy
Inheritance: AD, AR Classification: DEFINITIVE Submitted by: ClinGen
Ullrich congenital muscular dystrophy 1C
Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
dystonia 27
Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED, NO_KNOWN Submitted by: Illumina, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Orphanet
Ullrich congenital muscular dystrophy 1A
Inheritance: AR, AD, SD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp
Bethlem myopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Ullrich congenital muscular dystrophy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

COL6A3 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=-0.8).

BP6

Variant 2-237334726-G-A is Benign according to our data. Variant chr2-237334726-G-A is described in ClinVar as Benign. ClinVar VariationId is 95017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.59 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004369.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
COL6A3	NM_004369.4	MANE Select	c.9129C>T	p.Arg3043Arg	synonymous	Exon 41 of 44	NP_004360.2
COL6A3	NM_057167.4		c.8511C>T	p.Arg2837Arg	synonymous	Exon 40 of 43	NP_476508.2
COL6A3	NM_057166.5		c.7308C>T	p.Arg2436Arg	synonymous	Exon 38 of 41	NP_476507.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
COL6A3	ENST00000295550.9	TSL:1 MANE Select	c.9129C>T	p.Arg3043Arg	synonymous	Exon 41 of 44	ENSP00000295550.4
COL6A3	ENST00000472056.5	TSL:1	c.7308C>T	p.Arg2436Arg	synonymous	Exon 38 of 41	ENSP00000418285.1
COL6A3	ENST00000353578.9	TSL:5	c.8511C>T	p.Arg2837Arg	synonymous	Exon 40 of 43	ENSP00000315873.4

Frequencies

GnomAD3 genomes

AF:

0.0632

AC:

9608

AN:

152052

Hom.:

695

Cov.:

show subpopulations

Gnomad AFR

AF:

0.177

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0365

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.00425

Gnomad SAS

AF:

0.0220

Gnomad FIN

AF:

0.00735

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0190

Gnomad OTH

AF:

0.0604

GnomAD2 exomes

AF:

0.0313

AC:

7863

AN:

251444

AF XY:

0.0288

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.0250

Gnomad ASJ exome

AF:

0.0320

Gnomad EAS exome

AF:

0.00413

Gnomad FIN exome

AF:

0.00735

Gnomad NFE exome

AF:

0.0212

Gnomad OTH exome

AF:

0.0285

GnomAD4 exome

AF:

0.0223

AC:

32559

AN:

1461824

Hom.:

938

Cov.:

AF XY:

0.0219

AC XY:

15936

AN XY:

727210

show subpopulations

African (AFR)

AF:

0.187

AC:

6260

AN:

33480

American (AMR)

AF:

0.0259

AC:

1157

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0331

AC:

866

AN:

26136

East Asian (EAS)

AF:

0.00189

AC:

AN:

39700

South Asian (SAS)

AF:

0.0251

AC:

2169

AN:

86252

European-Finnish (FIN)

AF:

0.00887

AC:

474

AN:

53420

Middle Eastern (MID)

AF:

0.0632

AC:

361

AN:

5716

European-Non Finnish (NFE)

AF:

0.0173

AC:

19289

AN:

1112010

Other (OTH)

AF:

0.0316

AC:

1908

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

1860

3720

5580

7440

9300

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

806

1612

2418

3224

4030

<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:

0.0632

AC:

9618

AN:

152170

Hom.:

695

Cov.:

AF XY:

0.0610

AC XY:

4536

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.177

AC:

7327

AN:

41462

American (AMR)

AF:

0.0364

AC:

556

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0274

AC:

AN:

3470

East Asian (EAS)

AF:

0.00406

AC:

AN:

5168

South Asian (SAS)

AF:

0.0220

AC:

106

AN:

4818

European-Finnish (FIN)

AF:

0.00735

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0190

AC:

1292

AN:

68028

Other (OTH)

AF:

0.0598

AC:

126

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

421

841

1262

1682

2103

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.0409

Hom.:

210

Bravo

AF:

0.0712

Asia WGS

AF:

0.0230

AC:

AN:

3478

EpiCase

AF:

0.0235

EpiControl

AF:

0.0249

ClinVar

ClinVar submissions as Germline

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 (1)

Collagen 6-related myopathy (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.062

(source)

DANN

Benign

0.38

PhyloP100

-2.6

Mutation Taster

=100/0

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