Variant 11-7628409-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003621.5(PPFIBP2):c.888+63C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 1,457,538 control chromosomes in the GnomAD database, including 158,911 homozygotes. 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 0.51 ( 20732 hom., cov: 32)

Exomes 𝑓: 0.46 ( 138179 hom. )

Consequence

PPFIBP2
NM_003621.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.352

Variant links:

Genes affected

PPFIBP2 (HGNC:9250): (PPFIA binding protein 2) This gene encodes a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. The encoded protein is a beta liprin and plays a role in axon guidance and neuronal synapse development by recruiting LAR protein-tyrosine phosphatases to the plasma membrane. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

PPFIBP2 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=-0.67).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPFIBP2	NM_003621.5 linkuse as main transcript	c.888+63C>G		intron_variant		ENST00000299492.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPFIBP2	ENST00000299492.9 linkuse as main transcript	c.888+63C>G		intron_variant		1	NM_003621.5	P2	Q8ND30-1

Frequencies

GnomAD3 genomes

AF:

0.512

AC:

77780

AN:

151898

Hom.:

20712

Cov.:

show subpopulations

Gnomad AFR

AF:

0.670

Gnomad AMI

AF:

0.549

Gnomad AMR

AF:

0.441

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.619

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.517

GnomAD4 exome

AF:

0.457

AC:

596937

AN:

1305522

Hom.:

138179

AF XY:

0.454

AC XY:

298368

AN XY:

657188

show subpopulations

Gnomad4 AFR exome

AF:

0.686

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.486

Gnomad4 EAS exome

AF:

0.631

Gnomad4 SAS exome

AF:

0.357

Gnomad4 FIN exome

AF:

0.416

Gnomad4 NFE exome

AF:

0.455

Gnomad4 OTH exome

AF:

0.472

GnomAD4 genome

AF:

0.512

AC:

77841

AN:

152016

Hom.:

20732

Cov.:

AF XY:

0.507

AC XY:

37649

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.670

Gnomad4 AMR

AF:

0.441

Gnomad4 ASJ

AF:

0.481

Gnomad4 EAS

AF:

0.619

Gnomad4 SAS

AF:

0.348

Gnomad4 FIN

AF:

0.411

Gnomad4 NFE

AF:

0.452

Gnomad4 OTH

AF:

0.514

Alfa

AF:

0.307

Hom.:

687

Bravo

AF:

0.527

Asia WGS

AF:

0.461

AC:

1603

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.85

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