rs3213239
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001193621.3(PINLYP):c.-88_-85dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.63 ( 30159 hom., cov: 0)
Exomes 𝑓: 0.62 ( 55683 hom. )
Consequence
PINLYP
NM_001193621.3 5_prime_UTR
NM_001193621.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.94
Genes affected
PINLYP (HGNC:44206): (phospholipase A2 inhibitor and LY6/PLAUR domain containing) Predicted to enable phospholipase inhibitor activity. Predicted to be involved in negative regulation of catalytic activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
XRCC1 (HGNC:12828): (X-ray repair cross complementing 1) The protein encoded by this gene is involved in the efficient repair of DNA single-strand breaks formed by exposure to ionizing radiation and alkylating agents. This protein interacts with DNA ligase III, polymerase beta and poly (ADP-ribose) polymerase to participate in the base excision repair pathway. It may play a role in DNA processing during meiogenesis and recombination in germ cells. A rare microsatellite polymorphism in this gene is associated with cancer in patients of varying radiosensitivity. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PINLYP | NM_001193621.3 | c.-88_-85dup | 5_prime_UTR_variant | 1/6 | ENST00000599207.6 | ||
PINLYP | XM_047438830.1 | c.-211_-208dup | 5_prime_UTR_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PINLYP | ENST00000599207.6 | c.-88_-85dup | 5_prime_UTR_variant | 1/6 | 5 | NM_001193621.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.628 AC: 95042AN: 151248Hom.: 30144 Cov.: 0
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GnomAD4 exome AF: 0.616 AC: 172214AN: 279460Hom.: 55683 Cov.: 4 AF XY: 0.613 AC XY: 89371AN XY: 145734
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GnomAD4 genome ? AF: 0.628 AC: 95104AN: 151366Hom.: 30159 Cov.: 0 AF XY: 0.630 AC XY: 46602AN XY: 73940
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at