chr12-66123998-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_032338.4(LLPH):c.232G>A(p.Asp78Asn) 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
LLPH
NM_032338.4 missense
NM_032338.4 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: 5.12
Publications
0 publications found
Genes affected
LLPH (HGNC:28229): (LLP homolog, long-term synaptic facilitation factor) Enables RNA binding activity. Predicted to be involved in dendrite extension and positive regulation of dendritic spine development. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_032338.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| LLPH | TSL:1 MANE Select | c.232G>A | p.Asp78Asn | missense | Exon 3 of 3 | ENSP00000266604.2 | Q9BRT6 | ||
| ENSG00000228144 | TSL:2 | n.*362G>A | non_coding_transcript_exon | Exon 8 of 8 | ENSP00000454670.1 | F6UZH7 | |||
| ENSG00000228144 | TSL:2 | n.*362G>A | 3_prime_UTR | Exon 8 of 8 | ENSP00000454670.1 | F6UZH7 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000416 AC: 1AN: 240308 AF XY: 0.00000771 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
240308
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1451170Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 721624
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1451170
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
721624
African (AFR)
AF:
AC:
0
AN:
32716
American (AMR)
AF:
AC:
0
AN:
42686
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25730
East Asian (EAS)
AF:
AC:
0
AN:
39606
South Asian (SAS)
AF:
AC:
0
AN:
83486
European-Finnish (FIN)
AF:
AC:
0
AN:
53304
Middle Eastern (MID)
AF:
AC:
0
AN:
5718
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1108000
Other (OTH)
AF:
AC:
0
AN:
59924
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ExAC
AF:
AC:
1
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
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of ubiquitination at K83 (P = 0.0288)
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
DS_AL_spliceai
Position offset: 20
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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