rs12079994

chr1-247416606-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001243133.2(NLRP3):c.-749+413G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,856 control chromosomes in the GnomAD database, including 1,405 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 0.11 (1405 hom., cov: 31)
• Consequence: NLRP3 NM_001243133.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

Genes affected

NLRP3 (HGNC:16400): (NLR family pyrin domain containing 3) This gene encodes a pyrin-like protein containing a pyrin domain, a nucleotide-binding site (NBS) domain, and a leucine-rich repeat (LRR) motif. This protein interacts with the apoptosis-associated speck-like protein PYCARD/ASC, which contains a caspase recruitment domain, and is a member of the NLRP3 inflammasome complex. This complex functions as an upstream activator of NF-kappaB signaling, and it plays a role in the regulation of inflammation, the immune response, and apoptosis. The SARS-CoV 3a protein, a transmembrane pore-forming viroporin, has been shown to activate the NLRP3 inflammasome via the formation of ion channels in macrophages. Mutations in this gene are associated with familial cold autoinflammatory syndrome (FCAS), Muckle-Wells syndrome (MWS), chronic infantile neurological cutaneous and articular (CINCA) syndrome, neonatal-onset multisystem inflammatory disease (NOMID), keratoendotheliitis fugax hereditarian, and deafness, autosomal dominant 34, with or without inflammation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. Alternative 5' UTR structures are suggested by available data; however, insufficient evidence is available to determine if all of the represented 5' UTR splice patterns are biologically valid. [provided by RefSeq, Aug 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NLRP3	NM_001243133.2	c.-749+413G>A		intron_variant		ENST00000336119.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NLRP3	ENST00000336119.8	c.-749+413G>A		intron_variant		1	NM_001243133.2	P1
NLRP3	ENST00000391827.3	c.-749+413G>A		intron_variant		1
NLRP3	ENST00000391828.8	c.-107+413G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17137 AN: 151738 Hom.: 1400 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.107

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.113 AC: 17173 AN: 151856 Hom.: 1405 Cov.: 31 AF XY: 0.114 AC XY: 8438 AN XY: 74220

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0941

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0520

Gnomad4 FIN AF: 0.0873

Gnomad4 NFE AF: 0.0580

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0896 Hom.: 219

Bravo AF: 0.120

Asia WGS AF: 0.0900 AC: 311 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.0
Dann	Benign	0.31

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12079994; hg19: chr1-247579908;