1-148483024-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001123068.3(PPIAL4G):āc.229T>Cā(p.Ser77Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000781 in 1,612,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000053 ( 0 hom., cov: 28)
Exomes š: 0.000081 ( 0 hom. )
Consequence
PPIAL4G
NM_001123068.3 missense
NM_001123068.3 missense
Scores
1
4
12
Clinical Significance
Conservation
PhyloP100: 6.56
Genes affected
PPIAL4G (HGNC:33996): (peptidylprolyl isomerase A like 4G) Predicted to enable cyclosporin A binding activity and peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in protein folding and protein peptidyl-prolyl isomerization. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29124027).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPIAL4G | NM_001123068.3 | c.229T>C | p.Ser77Pro | missense_variant | 1/1 | ENST00000419275.3 | NP_001116540.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPIAL4G | ENST00000419275.3 | c.229T>C | p.Ser77Pro | missense_variant | 1/1 | NM_001123068.3 | ENSP00000393845 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152096Hom.: 0 Cov.: 28
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GnomAD3 exomes AF: 0.0000926 AC: 23AN: 248300Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135096
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GnomAD4 exome AF: 0.0000808 AC: 118AN: 1460790Hom.: 0 Cov.: 31 AF XY: 0.0000867 AC XY: 63AN XY: 726714
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152096Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 74302
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.229T>C (p.S77P) alteration is located in exon 1 (coding exon 1) of the PPIAL4G gene. This alteration results from a T to C substitution at nucleotide position 229, causing the serine (S) at amino acid position 77 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
Sift
Uncertain
D
Sift4G
Uncertain
D
Vest4
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at