Variant 19-10107354-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020230.7(PPAN):c.190-151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 738,918 control chromosomes in the GnomAD database, including 129,012 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.60 ( 27299 hom., cov: 33)

Exomes 𝑓: 0.58 ( 101713 hom. )

Consequence

PPAN
NM_020230.7 intron

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -1.21

Variant links:

Genes affected

PPAN (HGNC:9227): (peter pan homolog) The protein encoded by this gene is an evolutionarily conserved protein similar to yeast SSF1 as well as to the gene product of the Drosophila gene peter pan (ppan). SSF1 is known to be involved in the second step of mRNA splicing. Both SSF1 and ppan are essential for cell growth and proliferation. Exogenous expression of this gene was reported to reduce the anchorage-independent growth of some tumor cells. Read-through transcription of this gene with P2RY11/P2Y(11), an adjacent downstream gene that encodes an ATP receptor, has been found. These read-through transcripts are ubiquitously present and up-regulated during granulocyte differentiation. [provided by RefSeq, Nov 2010]

PPAN links:

PPAN-P2RY11 (HGNC:):

PPAN-P2RY11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPAN	NM_020230.7 linkuse as main transcript	c.190-151C>T		intron_variant		ENST00000253107.12	NP_064615.3
PPAN-P2RY11	NM_001198690.2 linkuse as main transcript	c.190-151C>T		intron_variant			NP_001185619.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
PPAN	ENST00000253107.12 linkuse as main transcript	c.190-151C>T	intron_variant	1	NM_020230.7	ENSP00000253107	P1	Q9NQ55-1
PPAN	ENST00000393793.5 linkuse as main transcript	c.31-151C>T	intron_variant	5		ENSP00000377382
PPAN	ENST00000430370.1 linkuse as main transcript	c.4-151C>T	intron_variant	3		ENSP00000415988
PPAN	ENST00000446223.5 linkuse as main transcript	c.4-151C>T	intron_variant	3		ENSP00000410485

Frequencies

GnomAD3 genomes

AF:

0.595

AC:

90484

AN:

151972

Hom.:

27266

Cov.:

show subpopulations

Gnomad AFR

AF:

0.608

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.655

Gnomad ASJ

AF:

0.559

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.691

Gnomad FIN

AF:

0.604

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.559

Gnomad OTH

AF:

0.619

GnomAD4 exome

AF:

0.585

AC:

343106

AN:

586826

Hom.:

101713

AF XY:

0.589

AC XY:

178518

AN XY:

303072

show subpopulations

Gnomad4 AFR exome

AF:

0.597

Gnomad4 AMR exome

AF:

0.684

Gnomad4 ASJ exome

AF:

0.552

Gnomad4 EAS exome

AF:

0.715

Gnomad4 SAS exome

AF:

0.677

Gnomad4 FIN exome

AF:

0.592

Gnomad4 NFE exome

AF:

0.558

Gnomad4 OTH exome

AF:

0.590

GnomAD4 genome

AF:

0.596

AC:

90577

AN:

152092

Hom.:

27299

Cov.:

AF XY:

0.601

AC XY:

44659

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.608

Gnomad4 AMR

AF:

0.654

Gnomad4 ASJ

AF:

0.559

Gnomad4 EAS

AF:

0.725

Gnomad4 SAS

AF:

0.691

Gnomad4 FIN

AF:

0.604

Gnomad4 NFE

AF:

0.559

Gnomad4 OTH

AF:

0.620

Alfa

AF:

0.569

Hom.:

31489

Bravo

AF:

0.602

Asia WGS

AF:

0.691

AC:

2403

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Cataplexy and narcolepsy

Other:1

association, no assertion criteria provided

case-control

Center for Narcolepsy, Stanford University

Dec 10, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.85

DANN

Benign

0.56

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over