rs7058353
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_006223.4(PIN4):c.-22C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.84 ( 28282 hom., 27016 hem., cov: 22)
Exomes 𝑓: 0.92 ( 317387 hom. 326155 hem. )
Failed GnomAD Quality Control
Consequence
PIN4
NM_006223.4 5_prime_UTR
NM_006223.4 5_prime_UTR
Scores
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.759
Genes affected
PIN4 (HGNC:8992): (peptidylprolyl cis/trans isomerase, NIMA-interacting 4) This gene encodes a member of the parvulin subfamily of the peptidyl-prolyl cis/trans isomerase protein family. The encoded protein catalyzes the isomerization of peptidylprolyl bonds, and may play a role in the cell cycle, chromatin remodeling, and/or ribosome biogenesis. The encoded protein may play an additional role in the mitochondria. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=2.1783342E-6).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIN4 | NM_006223.4 | c.-22C>A | 5_prime_UTR_variant | 1/4 | ENST00000373669.8 | ||
PIN4 | NM_001170747.1 | c.54C>A | p.Ser18Arg | missense_variant | 1/4 | ||
PIN4 | NR_033187.2 | n.8C>A | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIN4 | ENST00000373669.8 | c.-22C>A | 5_prime_UTR_variant | 1/4 | 1 | NM_006223.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.837 AC: 92180AN: 110069Hom.: 28290 Cov.: 22 AF XY: 0.831 AC XY: 26971AN XY: 32449
GnomAD3 genomes
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GnomAD3 exomes AF: 0.863 AC: 156944AN: 181775Hom.: 43880 AF XY: 0.868 AC XY: 57621AN XY: 66419
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.923 AC: 1003715AN: 1086911Hom.: 317387 Cov.: 30 AF XY: 0.918 AC XY: 326155AN XY: 355225
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Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.837 AC: 92210AN: 110123Hom.: 28282 Cov.: 22 AF XY: 0.831 AC XY: 27016AN XY: 32513
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2754
ESP6500AA
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2418
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6481
ExAC
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104411
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.;.
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.0
.;.;B
Vest4
MutPred
Loss of phosphorylation at S18 (P = 0.0375);Loss of phosphorylation at S18 (P = 0.0375);Loss of phosphorylation at S18 (P = 0.0375);
MPC
0.12
ClinPred
T
GERP RS
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