chr19-54927572-AAAAC-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001405531.1(NLRP7):c.2981+29_2981+32del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 1,607,956 control chromosomes in the GnomAD database, including 253,779 homozygotes. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: đť‘“ 0.55 ( 23404 hom., cov: 0)
Exomes đť‘“: 0.56 ( 230375 hom. )
Consequence
NLRP7
NM_001405531.1 intron
NM_001405531.1 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.260
Genes affected
NLRP7 (HGNC:22947): (NLR family pyrin domain containing 7) This gene encodes a member of the NACHT, leucine rich repeat, and PYD containing (NLRP) protein family. It has an N-terminal pyrin domain, followed by a NACHT domain, a NACHT-associated domain (NAD), and a C-terminal leucine-rich repeat (LRR) region. NLRP proteins are implicated in the activation of proinflammatory caspases through multiprotein complexes called inflammasomes. This gene may act as a feedback regulator of caspase-1-dependent interleukin 1-beta secretion. Alternative splicing results in multiple transcript variants encoding different isoforms. [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 = 0.693 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP7 | NM_001127255.2 | c.2981+29_2981+32del | intron_variant | ENST00000592784.6 | |||
NLRP7 | NM_001405531.1 | c.2981+29_2981+32del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP7 | ENST00000592784.6 | c.2981+29_2981+32del | intron_variant | 1 | NM_001127255.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.554 AC: 83739AN: 151210Hom.: 23382 Cov.: 0
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GnomAD3 exomes AF: 0.586 AC: 145854AN: 248942Hom.: 43313 AF XY: 0.586 AC XY: 79109AN XY: 134930
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GnomAD4 exome AF: 0.560 AC: 815566AN: 1456626Hom.: 230375 AF XY: 0.563 AC XY: 408197AN XY: 724760
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GnomAD4 genome ? AF: 0.554 AC: 83805AN: 151330Hom.: 23404 Cov.: 0 AF XY: 0.557 AC XY: 41140AN XY: 73880
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
Hydatidiform mole, recurrent, 1 Other:1
not provided, no classification provided | literature only | Unité médicale des maladies autoinflammatoires, CHRU Montpellier | - | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at