Variant rs11415 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_006223.4(PIN4):c.204C>T(p.Ala68Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 1,201,062 control chromosomes in the GnomAD database, including 6,104 homozygotes. There are 30,213 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1291 hom., 4485 hem., cov: 22)

Exomes 𝑓: 0.068 ( 4813 hom. 25728 hem. )

Consequence

PIN4
NM_006223.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

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]

PIN4 links:

PIN4 (HGNC:):

PIN4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant X-72196871-C-T is Benign according to our data. Variant chrX-72196871-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-1.16 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIN4	NM_006223.4 linkuse as main transcript	c.204C>T	p.Ala68Ala	synonymous_variant	3/4	ENST00000373669.8	NP_006214.3	Q9Y237-1
PIN4	NM_001170747.1 linkuse as main transcript	c.279C>T	p.Ala93Ala	synonymous_variant	3/4		NP_001164218.1	Q9Y237-3
PIN4	NR_033187.2 linkuse as main transcript	n.159C>T		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIN4	ENST00000373669.8 linkuse as main transcript	c.204C>T	p.Ala68Ala	synonymous_variant	3/4	1	NM_006223.4	ENSP00000362773.3		Q9Y237-1

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

14751

AN:

110830

Hom.:

1292

Cov.:

AF XY:

0.135

AC XY:

4466

AN XY:

33120

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.00436

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.0664

Gnomad EAS

AF:

0.479

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.0555

Gnomad MID

AF:

0.0720

Gnomad NFE

AF:

0.0337

Gnomad OTH

AF:

0.117

GnomAD3 exomes

AF:

0.122

AC:

22080

AN:

181535

Hom.:

1911

AF XY:

0.114

AC XY:

7529

AN XY:

66177

show subpopulations

Gnomad AFR exome

AF:

0.289

Gnomad AMR exome

AF:

0.133

Gnomad ASJ exome

AF:

0.0693

Gnomad EAS exome

AF:

0.457

Gnomad SAS exome

AF:

0.212

Gnomad FIN exome

AF:

0.0619

Gnomad NFE exome

AF:

0.0333

Gnomad OTH exome

AF:

0.0841

GnomAD4 exome

AF:

0.0679

AC:

74031

AN:

1090177

Hom.:

4813

Cov.:

AF XY:

0.0721

AC XY:

25728

AN XY:

356957

show subpopulations

Gnomad4 AFR exome

AF:

0.286

Gnomad4 AMR exome

AF:

0.138

Gnomad4 ASJ exome

AF:

0.0653

Gnomad4 EAS exome

AF:

0.475

Gnomad4 SAS exome

AF:

0.221

Gnomad4 FIN exome

AF:

0.0607

Gnomad4 NFE exome

AF:

0.0326

Gnomad4 OTH exome

AF:

0.0971

GnomAD4 genome

AF:

0.133

AC:

14772

AN:

110885

Hom.:

1291

Cov.:

AF XY:

0.135

AC XY:

4485

AN XY:

33183

show subpopulations

Gnomad4 AFR

AF:

0.280

Gnomad4 AMR

AF:

0.139

Gnomad4 ASJ

AF:

0.0664

Gnomad4 EAS

AF:

0.479

Gnomad4 SAS

AF:

0.243

Gnomad4 FIN

AF:

0.0555

Gnomad4 NFE

AF:

0.0337

Gnomad4 OTH

AF:

0.117

Alfa

AF:

0.0570

Hom.:

1701

Bravo

AF:

0.147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

2.0

DANN

Benign

0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over