chrX-154379496-C-A
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_000117.3(EMD):c.12C>A(p.Tyr4*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Y4Y) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 26)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
EMD
NM_000117.3 stop_gained
NM_000117.3 stop_gained
Scores
2
1
2
Clinical Significance
Conservation
PhyloP100: 0.796
Publications
0 publications found
Genes affected
EMD (HGNC:3331): (emerin) Emerin is a serine-rich nuclear membrane protein and a member of the nuclear lamina-associated protein family. It mediates membrane anchorage to the cytoskeleton. Dreifuss-Emery muscular dystrophy is an X-linked inherited degenerative myopathy resulting from mutation in the emerin gene. [provided by RefSeq, Jul 2008]
EMD Gene-Disease associations (from GenCC):
- X-linked Emery-Dreifuss muscular dystrophyInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- heart conduction diseaseInheritance: XL Classification: STRONG Submitted by: Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 86 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-154379496-C-A is Pathogenic according to our data. Variant chrX-154379496-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 804132.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
26
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1054407Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 344827
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1054407
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
344827
African (AFR)
AF:
AC:
0
AN:
24869
American (AMR)
AF:
AC:
0
AN:
28420
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18632
East Asian (EAS)
AF:
AC:
0
AN:
27178
South Asian (SAS)
AF:
AC:
0
AN:
50055
European-Finnish (FIN)
AF:
AC:
0
AN:
36890
Middle Eastern (MID)
AF:
AC:
0
AN:
4058
European-Non Finnish (NFE)
AF:
AC:
0
AN:
819957
Other (OTH)
AF:
AC:
0
AN:
44348
GnomAD4 genome
GnomAD4 genome
Cov.:
26
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
X-linked Emery-Dreifuss muscular dystrophy Pathogenic:1
May 28, 2019
Mendelics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
FATHMM_MKL
Benign
N
PhyloP100
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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