7-143139627-C-A
Variant names:
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
NM_002652.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.891
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]
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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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00127 AC: 193AN: 151980Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00298 AC: 750AN: 251296Hom.: 7 AF XY: 0.00266 AC XY: 361AN XY: 135812
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GnomAD4 exome AF: 0.00114 AC: 1662AN: 1458952Hom.: 17 Cov.: 31 AF XY: 0.00114 AC XY: 824AN XY: 725554
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GnomAD4 genome AF: 0.00127 AC: 193AN: 152098Hom.: 2 Cov.: 32 AF XY: 0.00132 AC XY: 98AN XY: 74362
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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
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at