Variant rs3087949 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001304331.2(PPFIA4):c.*2103C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,458 control chromosomes in the GnomAD database, including 44,500 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 0.76 ( 44369 hom., cov: 30)

Exomes 𝑓: 0.77 ( 131 hom. )

Consequence

PPFIA4
NM_001304331.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.816

Variant links:

Genes affected

PPFIA4 (HGNC:9248): (PTPRF interacting protein alpha 4) PPFIA4, or liprin-alpha-4, belongs to the liprin-alpha gene family. See liprin-alpha-1 (LIP1, or PPFIA1; MIM 611054) for background on liprins.[supplied by OMIM, Mar 2008]

PPFIA4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPFIA4	NM_001304331.2 linkuse as main transcript	c.*2103C>A		3_prime_UTR_variant	30/30	ENST00000295706.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPFIA4	ENST00000295706.9 linkuse as main transcript	c.*2103C>A		3_prime_UTR_variant	30/30	5	NM_001304331.2	P3

Frequencies

GnomAD3 genomes

AF:

0.761

AC:

115522

AN:

151886

Hom.:

44295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.859

Gnomad AMI

AF:

0.647

Gnomad AMR

AF:

0.750

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.734

Gnomad SAS

AF:

0.751

Gnomad FIN

AF:

0.779

Gnomad MID

AF:

0.759

Gnomad NFE

AF:

0.708

Gnomad OTH

AF:

0.752

GnomAD4 exome

AF:

0.771

AC:

350

AN:

454

Hom.:

131

Cov.:

AF XY:

0.763

AC XY:

206

AN XY:

270

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.771

Gnomad4 NFE exome

AF:

0.643

Gnomad4 OTH exome

AF:

0.875

GnomAD4 genome

AF:

0.761

AC:

115658

AN:

152004

Hom.:

44369

Cov.:

AF XY:

0.762

AC XY:

56633

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.860

Gnomad4 AMR

AF:

0.751

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.735

Gnomad4 SAS

AF:

0.752

Gnomad4 FIN

AF:

0.779

Gnomad4 NFE

AF:

0.708

Gnomad4 OTH

AF:

0.755

Alfa

AF:

0.720

Hom.:

53680

Bravo

AF:

0.766

Asia WGS

AF:

0.762

AC:

2649

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.057

DANN

Benign

0.55

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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