rs17333180
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002638.4(PI3):c.79+66C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 1,282,582 control chromosomes in the GnomAD database, including 17,689 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 0.15 ( 1923 hom., cov: 32)
Exomes 𝑓: 0.16 ( 15766 hom. )
Consequence
PI3
NM_002638.4 intron
NM_002638.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.11
Genes affected
PI3 (HGNC:8947): (peptidase inhibitor 3) This gene encodes an elastase-specific inhibitor that functions as an antimicrobial peptide against Gram-positive and Gram-negative bacteria, and fungal pathogens. The protein contains a WAP-type four-disulfide core (WFDC) domain, and is thus a member of the WFDC domain family. Most WFDC gene members are localized to chromosome 20q12-q13 in two clusters: centromeric and telomeric. This gene belongs to the centromeric cluster. Expression of this gene is upgulated by bacterial lipopolysaccharides and cytokines. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PI3 | NM_002638.4 | c.79+66C>A | intron_variant | ENST00000243924.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PI3 | ENST00000243924.4 | c.79+66C>A | intron_variant | 1 | NM_002638.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.153 AC: 23279AN: 152104Hom.: 1918 Cov.: 32
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GnomAD4 exome AF: 0.161 AC: 182054AN: 1130360Hom.: 15766 AF XY: 0.162 AC XY: 91718AN XY: 567072
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GnomAD4 genome ? AF: 0.153 AC: 23317AN: 152222Hom.: 1923 Cov.: 32 AF XY: 0.154 AC XY: 11479AN XY: 74404
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at