NM_001193621.3:c.-85_-84insGCCGGCCG
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001193621.3(PINLYP):c.-85_-84insGCCGGCCG 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 0.0000066 ( 0 hom., cov: 0)
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
Publications
21 publications found
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]
XRCC1 Gene-Disease associations (from GenCC):
- head and neck cancerInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- spinocerebellar ataxia, autosomal recessive 26Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PINLYP | ENST00000599207.6 | c.-85_-84insGCCGGCCG | 5_prime_UTR_variant | Exon 1 of 6 | 5 | NM_001193621.3 | ENSP00000469886.1 | |||
ENSG00000268361 | ENST00000594374.1 | c.169-15888_169-15887insGGCCGGCC | intron_variant | Intron 1 of 2 | 3 | ENSP00000472698.1 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151326Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151326
Hom.:
Cov.:
0
Gnomad AFR
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GnomAD4 exome Cov.: 4
GnomAD4 exome
Cov.:
4
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151326Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 73854 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151326
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
73854
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41134
American (AMR)
AF:
AC:
1
AN:
15210
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5116
South Asian (SAS)
AF:
AC:
0
AN:
4812
European-Finnish (FIN)
AF:
AC:
0
AN:
10464
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67830
Other (OTH)
AF:
AC:
0
AN:
2084
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
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0
1
1
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2
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0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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