rs776678940

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001848.3(COL6A1):​c.44G>A​(p.Cys15Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,454,048 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 29)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

COL6A1
NM_001848.3 missense

Scores

3
8
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.36
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COL6A1NM_001848.3 linkc.44G>A p.Cys15Tyr missense_variant Exon 1 of 35 ENST00000361866.8 NP_001839.2 P12109A0A384P5H7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COL6A1ENST00000361866.8 linkc.44G>A p.Cys15Tyr missense_variant Exon 1 of 35 1 NM_001848.3 ENSP00000355180.3 P12109

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
AF:
6.88e-7
AC:
1
AN:
1454048
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
722930
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.01e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
-0.080
CADD
Benign
18
DANN
Benign
0.96
DEOGEN2
Uncertain
0.59
D;T
Eigen
Benign
-0.036
Eigen_PC
Benign
-0.031
FATHMM_MKL
Benign
0.56
D
LIST_S2
Benign
0.52
T;T
M_CAP
Pathogenic
0.33
D
MetaRNN
Uncertain
0.43
T;T
MetaSVM
Benign
-0.31
T
MutationAssessor
Uncertain
2.1
M;.
PrimateAI
Pathogenic
0.81
D
PROVEAN
Uncertain
-2.7
D;.
REVEL
Uncertain
0.43
Sift
Uncertain
0.0030
D;.
Sift4G
Pathogenic
0.0010
D;D
Polyphen
0.98
D;.
Vest4
0.42
MutPred
0.48
Loss of catalytic residue at W16 (P = 0.0538);Loss of catalytic residue at W16 (P = 0.0538);
MVP
0.45
MPC
0.37
ClinPred
0.92
D
GERP RS
2.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6
Varity_R
0.45
gMVP
0.48

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr21-47401808; API