rs381809
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_134444.5(NLRP4):c.281-275C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 473,986 control chromosomes in the GnomAD database, including 45,001 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 0.43 ( 13999 hom., cov: 29)
Exomes 𝑓: 0.43 ( 31002 hom. )
Consequence
NLRP4
NM_134444.5 intron
NM_134444.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.485
Genes affected
NLRP4 (HGNC:22943): (NLR family pyrin domain containing 4) The protein encoded by this gene is a member of the nucleotide-binding and leucine-rich repeat receptor (NLR) family, and is predicted to contain an N-terminal pyrin effector domain (PYD), a centrally-located nucleotide-binding and oligomerization domain (NACHT) and C-terminal leucine-rich repeats (LRR). This gene product has a demonstrated role as a negative regulator of autophagy and type I interferon signaling pathways as a result of protein interactions with its NACHT domain. The PYD domain has also been shown to be important in the inhibition of NF-kB (nuclear factor kappa-light-chain-enhancer of activated B cells). [provided by RefSeq, Dec 2016]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP4 | NM_134444.5 | c.281-275C>T | intron_variant | ENST00000301295.11 | |||
NLRP4 | XM_017026344.1 | c.281-275C>T | intron_variant | ||||
NLRP4 | XM_017026345.1 | c.281-275C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP4 | ENST00000301295.11 | c.281-275C>T | intron_variant | 1 | NM_134444.5 | P1 | |||
NLRP4 | ENST00000587464.1 | c.281-275C>T | intron_variant | 2 | |||||
NLRP4 | ENST00000587891.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.428 AC: 64191AN: 150078Hom.: 13994 Cov.: 29
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GnomAD4 exome AF: 0.428 AC: 138596AN: 323788Hom.: 31002 Cov.: 0 AF XY: 0.429 AC XY: 71164AN XY: 166024
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GnomAD4 genome ? AF: 0.428 AC: 64224AN: 150198Hom.: 13999 Cov.: 29 AF XY: 0.435 AC XY: 31822AN XY: 73222
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ClinVar
Not reported inComputational 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