6-16129378-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013262.4(MYLIP):c.56C>A(p.Ala19Glu) variant causes a missense change. 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 (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MYLIP
NM_013262.4 missense
NM_013262.4 missense
Scores
2
4
12
Clinical Significance
Conservation
PhyloP100: 4.96
Publications
0 publications found
Genes affected
MYLIP (HGNC:21155): (myosin regulatory light chain interacting protein) The ERM protein family members ezrin, radixin, and moesin are cytoskeletal effector proteins linking actin to membrane-bound proteins at the cell surface. Myosin regulatory light chain interacting protein (MYLIP) is a novel ERM-like protein that interacts with myosin regulatory light chain and inhibits neurite outgrowth. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.24277699).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_013262.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MYLIP | TSL:1 MANE Select | c.56C>A | p.Ala19Glu | missense | Exon 1 of 7 | ENSP00000349298.3 | Q8WY64-1 | ||
| MYLIP | TSL:1 | n.56C>A | non_coding_transcript_exon | Exon 1 of 6 | ENSP00000008686.6 | Q5TIA5 | |||
| MYLIP | c.56C>A | p.Ala19Glu | missense | Exon 1 of 7 | ENSP00000520754.1 | A0ABB0MVE0 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1441978Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 715586
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1441978
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
715586
African (AFR)
AF:
AC:
0
AN:
33016
American (AMR)
AF:
AC:
0
AN:
42004
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25790
East Asian (EAS)
AF:
AC:
0
AN:
38690
South Asian (SAS)
AF:
AC:
0
AN:
83158
European-Finnish (FIN)
AF:
AC:
0
AN:
51698
Middle Eastern (MID)
AF:
AC:
0
AN:
5342
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1102766
Other (OTH)
AF:
AC:
0
AN:
59514
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of disorder (P = 0.0169)
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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