21-46116768-A-C

Variant names:

• chr21-46116768-A-C
• rs1555873084
• NM_001849.4:c.955-2A>C

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PVS1_Moderate PM2 PP5_Moderate

The NM_001849.4(COL6A2):​c.955-2A>C variant causes a splice acceptor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: COL6A2 NM_001849.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 6.19
• Publications: 1 publications found

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, 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: AD, AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• 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

ACMG classification

Our verdict: Likely_pathogenic. The variant received 6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.014705882 fraction of the gene. Cryptic splice site detected, with MaxEntScore 8, offset of -48, new splice context is: ccctccttcctgctgctcAGggc. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 21-46116768-A-C is Pathogenic according to our data. Variant chr21-46116768-A-C is described in ClinVar as Pathogenic. ClinVar VariationId is 1691316.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL6A2	NM_001849.4	c.955-2A>C		splice_acceptor_variant, intron_variant	Intron 9 of 27	ENST00000300527.9	NP_001840.3
COL6A2	NM_058174.3	c.955-2A>C		splice_acceptor_variant, intron_variant	Intron 9 of 27		NP_478054.2
COL6A2	NM_058175.3	c.955-2A>C		splice_acceptor_variant, intron_variant	Intron 9 of 27		NP_478055.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL6A2	ENST00000300527.9	c.955-2A>C		splice_acceptor_variant, intron_variant	Intron 9 of 27	1	NM_001849.4	ENSP00000300527.4
COL6A2	ENST00000397763.6	c.955-2A>C		splice_acceptor_variant, intron_variant	Intron 9 of 27	5		ENSP00000380870.1
COL6A2	ENST00000409416.6	c.955-2A>C		splice_acceptor_variant, intron_variant	Intron 8 of 26	5		ENSP00000387115.1
COL6A2	ENST00000485591.1	n.611-2A>C		splice_acceptor_variant, intron_variant	Intron 5 of 6	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Ullrich congenital muscular dystrophy 1A;CN029274:Bethlem myopathy 1A Pathogenic:1

May 18, 2022

Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.955-2A>C variant is not present in publicly available population databases like 1000 Genomes, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), Genome Aggregation Database (gnomAD) and Indian Exome Database. The variant is not present in our in-house exome database. The variant was previously identified in similarly affected patients, published in literatures (PMID: 34167565, 29419890, 27453230, 20976770, 18366090, 15689448) and reported to Human Genome Mutation Database (HGMD ID: CS050380). In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome, HSF3.1 etc. predicted this variant to be likely deleterious. Different algorithms to predict mRNA splicing abnormalities, predicted this variant to potentially affect splicing. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Benign	-0.17
CADD	Pathogenic	32
DANN	Uncertain	0.98
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Uncertain	0.97	D
PhyloP100		6.2
GERP RS		4.1
Mutation Taster		=0/100	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.80
SpliceAI score (max)		0.98		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.56		Position offset: 26
DS_AL_spliceai		0.98		Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1555873084; hg19: chr21-47536682;