chr1-13223386-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_001099850.2(PRAMEF18):c.1386G>A(p.Thr462Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 3)
Exomes 𝑓: 0.000024 ( 8 hom. )
Failed GnomAD Quality Control
Consequence
PRAMEF18
NM_001099850.2 synonymous
NM_001099850.2 synonymous
Scores
1
Clinical Significance
Conservation
PhyloP100: -3.71
Publications
0 publications found
Genes affected
PRAMEF18 (HGNC:30693): (PRAME family member 18) Predicted to be involved in several processes, including negative regulation of apoptotic process; negative regulation of transcription, DNA-templated; and positive regulation of cell population proliferation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP7
Synonymous conserved (PhyloP=-3.71 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001099850.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PRAMEF18 | NM_001099850.2 | MANE Select | c.1386G>A | p.Thr462Thr | synonymous | Exon 3 of 3 | NP_001093320.2 | Q5VWM3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PRAMEF18 | ENST00000624297.3 | TSL:1 MANE Select | c.1386G>A | p.Thr462Thr | synonymous | Exon 3 of 3 | ENSP00000485473.2 | Q5VWM3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
3
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000243 AC: 30AN: 1234922Hom.: 8 Cov.: 28 AF XY: 0.0000293 AC XY: 18AN XY: 614252 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
30
AN:
1234922
Hom.:
Cov.:
28
AF XY:
AC XY:
18
AN XY:
614252
show subpopulations
African (AFR)
AF:
AC:
0
AN:
28000
American (AMR)
AF:
AC:
0
AN:
36312
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19694
East Asian (EAS)
AF:
AC:
0
AN:
22202
South Asian (SAS)
AF:
AC:
0
AN:
78228
European-Finnish (FIN)
AF:
AC:
0
AN:
40604
Middle Eastern (MID)
AF:
AC:
0
AN:
3244
European-Non Finnish (NFE)
AF:
AC:
29
AN:
958722
Other (OTH)
AF:
AC:
1
AN:
47916
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.632
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
3
Alfa
AF:
Hom.:
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
BayesDel_noAF
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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