rs17042882
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001144382.2(PLCL2):c.327+45018C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 152,206 control chromosomes in the GnomAD database, including 24 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 0.015 ( 24 hom., cov: 32)
Consequence
PLCL2
NM_001144382.2 intron
NM_001144382.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.277
Genes affected
PLCL2 (HGNC:9064): (phospholipase C like 2) Enables GABA receptor binding activity. Predicted to be involved in negative regulation of cold-induced thermogenesis and phosphatidylinositol-mediated signaling. Predicted to act upstream of or within several processes, including B cell activation; gamma-aminobutyric acid signaling pathway; and negative regulation of B cell receptor signaling pathway. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.72).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0152 (2318/152206) while in subpopulation NFE AF= 0.0269 (1827/68006). AF 95% confidence interval is 0.0258. There are 24 homozygotes in gnomad4. There are 1077 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2321 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCL2 | NM_001144382.2 | c.327+45018C>A | intron_variant | ENST00000615277.5 | |||
PLCL2 | XM_047447799.1 | c.-6480C>A | 5_prime_UTR_variant | 1/7 | |||
PLCL2 | XM_006713073.4 | c.12+30700C>A | intron_variant | ||||
PLCL2 | XM_017006025.2 | c.-155-7171C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCL2 | ENST00000615277.5 | c.327+45018C>A | intron_variant | 1 | NM_001144382.2 | ||||
PLCL2 | ENST00000460467.1 | n.439-79290C>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0153 AC: 2321AN: 152090Hom.: 24 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0152 AC: 2318AN: 152206Hom.: 24 Cov.: 32 AF XY: 0.0145 AC XY: 1077AN XY: 74442
GnomAD4 genome
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1077
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at