chr21-45981846-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001848.3(COL6A1):​c.-5C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 1,574,586 control chromosomes in the GnomAD database, including 216,813 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 18376 hom., cov: 24)
Exomes 𝑓: 0.52 ( 198437 hom. )

Consequence

COL6A1
NM_001848.3 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.257
Variant links:
Genes affected
COL6A1 (HGNC:2211): (collagen type VI alpha 1 chain) The collagens are a superfamily of proteins that play a role in maintaining the integrity of various tissues. Collagens are extracellular matrix proteins and have a triple-helical domain as their common structural element. Collagen VI is a major structural component of microfibrils. The basic structural unit of collagen VI is a heterotrimer of the alpha1(VI), alpha2(VI), and alpha3(VI) chains. The alpha2(VI) and alpha3(VI) chains are encoded by the COL6A2 and COL6A3 genes, respectively. The protein encoded by this gene is the alpha 1 subunit of type VI collagen (alpha1(VI) chain). Mutations in the genes that code for the collagen VI subunits result in the autosomal dominant disorder, Bethlem myopathy. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 21-45981846-C-G is Benign according to our data. Variant chr21-45981846-C-G is described in ClinVar as [Benign]. Clinvar id is 93792.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-45981846-C-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COL6A1NM_001848.3 linkuse as main transcriptc.-5C>G 5_prime_UTR_variant 1/35 ENST00000361866.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COL6A1ENST00000361866.8 linkuse as main transcriptc.-5C>G 5_prime_UTR_variant 1/351 NM_001848.3 P1

Frequencies

GnomAD3 genomes
AF:
0.477
AC:
71156
AN:
149192
Hom.:
18365
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.284
Gnomad AMI
AF:
0.605
Gnomad AMR
AF:
0.556
Gnomad ASJ
AF:
0.583
Gnomad EAS
AF:
0.770
Gnomad SAS
AF:
0.621
Gnomad FIN
AF:
0.562
Gnomad MID
AF:
0.660
Gnomad NFE
AF:
0.521
Gnomad OTH
AF:
0.539
GnomAD3 exomes
AF:
0.555
AC:
104340
AN:
188092
Hom.:
29837
AF XY:
0.557
AC XY:
57300
AN XY:
102834
show subpopulations
Gnomad AFR exome
AF:
0.270
Gnomad AMR exome
AF:
0.604
Gnomad ASJ exome
AF:
0.573
Gnomad EAS exome
AF:
0.774
Gnomad SAS exome
AF:
0.604
Gnomad FIN exome
AF:
0.557
Gnomad NFE exome
AF:
0.516
Gnomad OTH exome
AF:
0.576
GnomAD4 exome
AF:
0.523
AC:
744998
AN:
1425282
Hom.:
198437
Cov.:
34
AF XY:
0.527
AC XY:
372074
AN XY:
706378
show subpopulations
Gnomad4 AFR exome
AF:
0.272
Gnomad4 AMR exome
AF:
0.604
Gnomad4 ASJ exome
AF:
0.580
Gnomad4 EAS exome
AF:
0.748
Gnomad4 SAS exome
AF:
0.606
Gnomad4 FIN exome
AF:
0.563
Gnomad4 NFE exome
AF:
0.509
Gnomad4 OTH exome
AF:
0.539
GnomAD4 genome
AF:
0.477
AC:
71194
AN:
149304
Hom.:
18376
Cov.:
24
AF XY:
0.482
AC XY:
35079
AN XY:
72772
show subpopulations
Gnomad4 AFR
AF:
0.284
Gnomad4 AMR
AF:
0.555
Gnomad4 ASJ
AF:
0.583
Gnomad4 EAS
AF:
0.770
Gnomad4 SAS
AF:
0.619
Gnomad4 FIN
AF:
0.562
Gnomad4 NFE
AF:
0.521
Gnomad4 OTH
AF:
0.544
Alfa
AF:
0.490
Hom.:
5441
Bravo
AF:
0.470
Asia WGS
AF:
0.703
AC:
2443
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:7
Benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoAug 15, 2013- -
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)May 20, 2016- -
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Benign, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Benign, criteria provided, single submitterclinical testingGeneDxJan 25, 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. -
Collagen 6-related myopathy Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 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
-0.90
CADD
Benign
8.7
DANN
Benign
0.48
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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: rs7671; hg19: chr21-47401760; API