chr11-7535346-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003621.5(PPFIBP2):​c.-36-14094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 152,290 control chromosomes in the GnomAD database, including 518 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 0.068 ( 518 hom., cov: 33)

Consequence

PPFIBP2
NM_003621.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.625

Publications

12 publications found
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]

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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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PPFIBP2NM_003621.5 linkc.-36-14094A>G intron_variant Intron 1 of 23 ENST00000299492.9 NP_003612.3 Q8ND30-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PPFIBP2ENST00000299492.9 linkc.-36-14094A>G intron_variant Intron 1 of 23 1 NM_003621.5 ENSP00000299492.4 Q8ND30-1
PPFIBP2ENST00000684123.1 linkc.-36-14094A>G intron_variant Intron 1 of 26 ENSP00000507842.1 A0A804HKA2
PPFIBP2ENST00000526873.5 linkc.-36-14094A>G intron_variant Intron 1 of 2 4 ENSP00000434641.1 E9PK17
PPFIBP2ENST00000528947.5 linkc.-192-12998A>G intron_variant Intron 1 of 3 2 ENSP00000431724.1 E9PK17

Frequencies

GnomAD3 genomes
AF:
0.0684
AC:
10413
AN:
152172
Hom.:
512
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0177
Gnomad AMI
AF:
0.0439
Gnomad AMR
AF:
0.163
Gnomad ASJ
AF:
0.0931
Gnomad EAS
AF:
0.116
Gnomad SAS
AF:
0.136
Gnomad FIN
AF:
0.0829
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0661
Gnomad OTH
AF:
0.0866
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0685
AC:
10427
AN:
152290
Hom.:
518
Cov.:
33
AF XY:
0.0721
AC XY:
5371
AN XY:
74474
show subpopulations
African (AFR)
AF:
0.0176
AC:
733
AN:
41578
American (AMR)
AF:
0.164
AC:
2506
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.0931
AC:
323
AN:
3470
East Asian (EAS)
AF:
0.116
AC:
602
AN:
5172
South Asian (SAS)
AF:
0.136
AC:
659
AN:
4830
European-Finnish (FIN)
AF:
0.0829
AC:
880
AN:
10614
Middle Eastern (MID)
AF:
0.0306
AC:
9
AN:
294
European-Non Finnish (NFE)
AF:
0.0661
AC:
4496
AN:
68022
Other (OTH)
AF:
0.0848
AC:
179
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
485
970
1455
1940
2425
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
128
256
384
512
640
<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:
0.0722
Hom.:
964
Bravo
AF:
0.0715
Asia WGS
AF:
0.125
AC:
435
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.41
DANN
Benign
0.29
PhyloP100
-0.63
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs12791447; hg19: chr11-7556577; API