2-27079228-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_007046.4(EMILIN1):c.163C>A(p.Arg55Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R55H) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
EMILIN1
NM_007046.4 missense
NM_007046.4 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 0.514
Publications
2 publications found
Genes affected
EMILIN1 (HGNC:19880): (elastin microfibril interfacer 1) This gene encodes an extracellular matrix glycoprotein that is characterized by an N-terminal microfibril interface domain, a coiled-coiled alpha-helical domain, a collagenous domain and a C-terminal globular C1q domain. The encoded protein associates with elastic fibers at the interface between elastin and microfibrils and may play a role in the development of elastic tissues including large blood vessels, dermis, heart and lung. [provided by RefSeq, Sep 2009]
EMILIN1 Gene-Disease associations (from GenCC):
- neuronopathy, distal hereditary motor, autosomal dominant 10Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.42030466).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1410802Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 702134
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1410802
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
702134
African (AFR)
AF:
AC:
0
AN:
28692
American (AMR)
AF:
AC:
0
AN:
33542
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24150
East Asian (EAS)
AF:
AC:
0
AN:
34806
South Asian (SAS)
AF:
AC:
0
AN:
81340
European-Finnish (FIN)
AF:
AC:
0
AN:
51480
Middle Eastern (MID)
AF:
AC:
0
AN:
5590
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1093216
Other (OTH)
AF:
AC:
0
AN:
57986
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Jan 22, 2024
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
PM2, PP3 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Pathogenic
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of catalytic residue at R55 (P = 0.0121);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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