dbSNP rs3087949: PPFIA4:c.*2103C>A (chr1-203078493-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

18 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304331.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PPFIA4	NM_001304331.2	MANE Select	c.*2103C>A	3_prime_UTR	Exon 30 of 30	NP_001291260.1
PPFIA4	NM_001304332.2		c.*2103C>A	3_prime_UTR	Exon 29 of 29	NP_001291261.1
PPFIA4	NM_001393950.1		c.*2103C>A	3_prime_UTR	Exon 30 of 30	NP_001380879.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PPFIA4	ENST00000295706.9	TSL:5 MANE Select	c.*2103C>A	3_prime_UTR	Exon 30 of 30	ENSP00000295706.5
PPFIA4	ENST00000447715.6	TSL:1	c.*2103C>A	3_prime_UTR	Exon 35 of 35	ENSP00000402576.1
PPFIA4	ENST00000272198.10	TSL:1	c.*2103C>A	3_prime_UTR	Exon 17 of 17	ENSP00000272198.6

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

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.771

AC:

330

AN:

428

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.643

AC:

AN:

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.761

AC:

115658

AN:

152004

Hom.:

44369

Cov.:

AF XY:

0.762

AC XY:

56633

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.860

AC:

35655

AN:

41480

American (AMR)

AF:

0.751

AC:

11472

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.699

AC:

2425

AN:

3470

East Asian (EAS)

AF:

0.735

AC:

3796

AN:

5166

South Asian (SAS)

AF:

0.752

AC:

3611

AN:

4802

European-Finnish (FIN)

AF:

0.779

AC:

8221

AN:

10560

Middle Eastern (MID)

AF:

0.759

AC:

223

AN:

294

European-Non Finnish (NFE)

AF:

0.708

AC:

48078

AN:

67938

Other (OTH)

AF:

0.755

AC:

1591

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1370

2740

4111

5481

6851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

854

1708

2562

3416

4270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.725

Hom.:

68738

Bravo

AF:

0.766

Asia WGS

AF:

0.762

AC:

2649

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.057

(source)

DANN

Benign

0.55

PhyloP100

-0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over