7-143139627-C-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002652.3(PIP):​c.426C>A​(p.Ile142Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,611,050 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 17 hom. )

Consequence

PIP
NM_002652.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.891
Variant links:
Genes affected
PIP (HGNC:8993): (prolactin induced protein) Enables IgG binding activity; aspartic-type endopeptidase activity; and identical protein binding activity. Involved in several processes, including detection of chemical stimulus involved in sensory perception of bitter taste; negative regulation of T cell apoptotic process; and proteolysis. Located in extracellular space and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 7-143139627-C-A is Benign according to our data. Variant chr7-143139627-C-A is described in ClinVar as [Benign]. Clinvar id is 712563.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.891 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PIPNM_002652.3 linkc.426C>A p.Ile142Ile synonymous_variant Exon 4 of 4 ENST00000291009.4 NP_002643.1 P12273

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PIPENST00000291009.4 linkc.426C>A p.Ile142Ile synonymous_variant Exon 4 of 4 1 NM_002652.3 ENSP00000291009.3 P12273

Frequencies

GnomAD3 genomes
AF:
0.00127
AC:
193
AN:
151980
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00439
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00311
Gnomad FIN
AF:
0.00255
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000765
Gnomad OTH
AF:
0.000481
GnomAD3 exomes
AF:
0.00298
AC:
750
AN:
251296
Hom.:
7
AF XY:
0.00266
AC XY:
361
AN XY:
135812
show subpopulations
Gnomad AFR exome
AF:
0.000738
Gnomad AMR exome
AF:
0.0138
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000326
Gnomad SAS exome
AF:
0.00235
Gnomad FIN exome
AF:
0.00314
Gnomad NFE exome
AF:
0.000889
Gnomad OTH exome
AF:
0.00212
GnomAD4 exome
AF:
0.00114
AC:
1662
AN:
1458952
Hom.:
17
Cov.:
31
AF XY:
0.00114
AC XY:
824
AN XY:
725554
show subpopulations
Gnomad4 AFR exome
AF:
0.000568
Gnomad4 AMR exome
AF:
0.0122
Gnomad4 ASJ exome
AF:
0.0000768
Gnomad4 EAS exome
AF:
0.000479
Gnomad4 SAS exome
AF:
0.00246
Gnomad4 FIN exome
AF:
0.00281
Gnomad4 NFE exome
AF:
0.000594
Gnomad4 OTH exome
AF:
0.000913
GnomAD4 genome
AF:
0.00127
AC:
193
AN:
152098
Hom.:
2
Cov.:
32
AF XY:
0.00132
AC XY:
98
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.000723
Gnomad4 AMR
AF:
0.00439
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00311
Gnomad4 FIN
AF:
0.00255
Gnomad4 NFE
AF:
0.000765
Gnomad4 OTH
AF:
0.000476
Alfa
AF:
0.000945
Hom.:
0
Bravo
AF:
0.00151
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.000766
EpiControl
AF:
0.000593

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jul 06, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
0.10
DANN
Benign
0.64

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.

Other links and lift over

dbSNP: rs147384445; hg19: chr7-142836720; API