Genetic Variant NM_001304331.2:c.*1157G>C (chr1-203077547-G-C) – 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.*1157G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,160 control chromosomes in the GnomAD database, including 1,689 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 0.13 ( 1688 hom., cov: 32)

Exomes 𝑓: 0.56 ( 1 hom. )

Consequence

PPFIA4
NM_001304331.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.100

Publications

7 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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 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.*1157G>C	3_prime_UTR	Exon 30 of 30	NP_001291260.1
PPFIA4	NM_001304332.2		c.*1157G>C	3_prime_UTR	Exon 29 of 29	NP_001291261.1
PPFIA4	NM_001393950.1		c.*1157G>C	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.*1157G>C	3_prime_UTR	Exon 30 of 30	ENSP00000295706.5
PPFIA4	ENST00000447715.6	TSL:1	c.*1157G>C	3_prime_UTR	Exon 35 of 35	ENSP00000402576.1
PPFIA4	ENST00000272198.10	TSL:1	c.*1157G>C	3_prime_UTR	Exon 17 of 17	ENSP00000272198.6

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19978

AN:

152026

Hom.:

1689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0411

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.0819

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.139

GnomAD4 exome

AF:

0.563

AC:

AN:

Hom.:

Cov.:

AF XY:

0.583

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.571

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.632

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.131

AC:

19988

AN:

152144

Hom.:

1688

Cov.:

AF XY:

0.135

AC XY:

10017

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.0412

AC:

1712

AN:

41526

American (AMR)

AF:

0.159

AC:

2426

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

723

AN:

3466

East Asian (EAS)

AF:

0.0821

AC:

423

AN:

5154

South Asian (SAS)

AF:

0.241

AC:

1158

AN:

4802

European-Finnish (FIN)

AF:

0.175

AC:

1853

AN:

10586

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.165

AC:

11237

AN:

67996

Other (OTH)

AF:

0.138

AC:

292

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

839

1679

2518

3358

4197

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.145

Hom.:

239

Bravo

AF:

0.123

Asia WGS

AF:

0.142

AC:

495

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.0

(source)

DANN

Benign

0.40

PhyloP100

0.10

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over