X-72181764-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_006223.4(PIN4):​c.-22C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)

Consequence

PIN4
NM_006223.4 5_prime_UTR

Scores

15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.759
Variant links:
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 -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.036812305).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIN4NM_006223.4 linkuse as main transcriptc.-22C>G 5_prime_UTR_variant 1/4 ENST00000373669.8
PIN4NM_001170747.1 linkuse as main transcriptc.54C>G p.Ser18Arg missense_variant 1/4
PIN4NR_033187.2 linkuse as main transcriptn.8C>G non_coding_transcript_exon_variant 1/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIN4ENST00000373669.8 linkuse as main transcriptc.-22C>G 5_prime_UTR_variant 1/41 NM_006223.4 P1Q9Y237-1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.62
T
BayesDel_noAF
Benign
-1.1
CADD
Benign
2.2
DANN
Benign
0.42
DEOGEN2
Benign
0.042
T;.;.
FATHMM_MKL
Benign
0.11
N
LIST_S2
Benign
0.26
.;T;T
M_CAP
Benign
0.0035
T
MetaRNN
Benign
0.037
T;T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
1.0
P;P;P
PrimateAI
Benign
0.33
T
PROVEAN
Benign
0.64
N;N;N
REVEL
Benign
0.0080
Sift
Benign
1.0
T;T;T
Sift4G
Benign
0.90
T;T;T
Polyphen
0.0
.;.;B
Vest4
0.12
MutPred
0.30
Loss of phosphorylation at S18 (P = 0.0375);Loss of phosphorylation at S18 (P = 0.0375);Loss of phosphorylation at S18 (P = 0.0375);
MVP
0.043
MPC
0.12
ClinPred
0.015
T
GERP RS
-4.8
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7058353; hg19: chrX-71401614; API