2-237340465-T-C

Variant summary

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

The NM_004369.4(COL6A3):ā€‹c.8451A>Gā€‹(p.Pro2817Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 1,612,866 control chromosomes in the GnomAD database, including 8,121 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.069 ( 472 hom., cov: 32)
Exomes š‘“: 0.097 ( 7649 hom. )

Consequence

COL6A3
NM_004369.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -6.63
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BP6
Variant 2-237340465-T-C is Benign according to our data. Variant chr2-237340465-T-C is described in ClinVar as [Benign]. Clinvar id is 95003.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-237340465-T-C is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-6.63 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL6A3NM_004369.4 linkc.8451A>G p.Pro2817Pro synonymous_variant 38/44 ENST00000295550.9 NP_004360.2 P12111-1D9ZGF2Q8N4Z1Q63HQ4
COL6A3NM_057167.4 linkc.7833A>G p.Pro2611Pro synonymous_variant 37/43 NP_476508.2 P12111-2Q8N4Z1Q63HQ4
COL6A3NM_057166.5 linkc.6630A>G p.Pro2210Pro synonymous_variant 35/41 NP_476507.3 P12111-4B7ZW00

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL6A3ENST00000295550.9 linkc.8451A>G p.Pro2817Pro synonymous_variant 38/441 NM_004369.4 ENSP00000295550.4 P12111-1

Frequencies

GnomAD3 genomes
AF:
0.0687
AC:
10451
AN:
152150
Hom.:
472
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0189
Gnomad AMI
AF:
0.139
Gnomad AMR
AF:
0.0489
Gnomad ASJ
AF:
0.105
Gnomad EAS
AF:
0.00945
Gnomad SAS
AF:
0.0636
Gnomad FIN
AF:
0.0914
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.102
Gnomad OTH
AF:
0.0641
GnomAD3 exomes
AF:
0.0745
AC:
18646
AN:
250156
Hom.:
868
AF XY:
0.0770
AC XY:
10427
AN XY:
135338
show subpopulations
Gnomad AFR exome
AF:
0.0177
Gnomad AMR exome
AF:
0.0391
Gnomad ASJ exome
AF:
0.107
Gnomad EAS exome
AF:
0.0101
Gnomad SAS exome
AF:
0.0636
Gnomad FIN exome
AF:
0.0934
Gnomad NFE exome
AF:
0.101
Gnomad OTH exome
AF:
0.0743
GnomAD4 exome
AF:
0.0972
AC:
141954
AN:
1460598
Hom.:
7649
Cov.:
32
AF XY:
0.0963
AC XY:
69948
AN XY:
726676
show subpopulations
Gnomad4 AFR exome
AF:
0.0158
Gnomad4 AMR exome
AF:
0.0413
Gnomad4 ASJ exome
AF:
0.111
Gnomad4 EAS exome
AF:
0.00967
Gnomad4 SAS exome
AF:
0.0650
Gnomad4 FIN exome
AF:
0.0925
Gnomad4 NFE exome
AF:
0.108
Gnomad4 OTH exome
AF:
0.0889
GnomAD4 genome
AF:
0.0686
AC:
10445
AN:
152268
Hom.:
472
Cov.:
32
AF XY:
0.0669
AC XY:
4978
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0188
Gnomad4 AMR
AF:
0.0488
Gnomad4 ASJ
AF:
0.105
Gnomad4 EAS
AF:
0.00947
Gnomad4 SAS
AF:
0.0634
Gnomad4 FIN
AF:
0.0914
Gnomad4 NFE
AF:
0.102
Gnomad4 OTH
AF:
0.0629
Alfa
AF:
0.0897
Hom.:
345
Bravo
AF:
0.0647
Asia WGS
AF:
0.0430
AC:
151
AN:
3478
EpiCase
AF:
0.101
EpiControl
AF:
0.0999

ClinVar

Significance: Benign
Submissions summary: Benign:10
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:6
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Aug 07, 2012- -
Benign, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Likely benign, no assertion criteria providedclinical testingGenetic Services Laboratory, University of Chicago-Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Benign, criteria provided, single submitterclinical testingGeneDxJan 05, 2016This 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. -
not provided Benign:2
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsSep 13, 2017- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Bethlem myopathy 1A Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Collagen 6-related myopathy Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.0020
DANN
Benign
0.41

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.

Other links and lift over

dbSNP: rs61729844; hg19: chr2-238249108; COSMIC: COSV55108426; API