rs104895559
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1
The NM_001405531.1(NLRP7):c.1456_1457insG(p.Glu486GlyfsTer42) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as not provided (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes đť‘“: 0.0000021 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NLRP7
NM_001405531.1 frameshift
NM_001405531.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.544
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 Likely_pathogenic. Variant got 8 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP7 | NM_001127255.2 | c.1456_1457insG | p.Glu486GlyfsTer42 | frameshift_variant | 4/11 | ENST00000592784.6 | |
NLRP7 | NM_001405531.1 | c.1456_1457insG | p.Glu486GlyfsTer42 | frameshift_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP7 | ENST00000592784.6 | c.1456_1457insG | p.Glu486GlyfsTer42 | frameshift_variant | 4/11 | 1 | NM_001127255.2 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000205 AC: 3AN: 1461788Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727204
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
3
AN:
1461788
Hom.:
Cov.:
35
AF XY:
AC XY:
2
AN XY:
727204
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
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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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at