chr19-54923899-TC-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001405531.1(NLRP7):c.2982-28del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0908 in 1,611,612 control chromosomes in the GnomAD database, including 9,093 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.12 ( 1363 hom., cov: 30)
Exomes 𝑓: 0.088 ( 7730 hom. )
Consequence
NLRP7
NM_001405531.1 intron
NM_001405531.1 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.799
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 -10 ACMG points.
BP6
?
Variant 19-54923899-TC-T is Benign according to our data. Variant chr19-54923899-TC-T is described in ClinVar as [Likely_benign]. Clinvar id is 997712.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP7 | NM_001127255.2 | c.2982-28del | intron_variant | ENST00000592784.6 | |||
NLRP7 | NM_001405531.1 | c.2982-28del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP7 | ENST00000592784.6 | c.2982-28del | intron_variant | 1 | NM_001127255.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.118 AC: 17997AN: 152030Hom.: 1356 Cov.: 30
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GnomAD3 exomes AF: 0.123 AC: 30541AN: 248580Hom.: 2725 AF XY: 0.113 AC XY: 15213AN XY: 134680
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GnomAD4 exome AF: 0.0879 AC: 128243AN: 1459464Hom.: 7730 Cov.: 28 AF XY: 0.0855 AC XY: 62092AN XY: 726178
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GnomAD4 genome ? AF: 0.119 AC: 18038AN: 152148Hom.: 1363 Cov.: 30 AF XY: 0.124 AC XY: 9224AN XY: 74392
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hydatidiform mole Benign:1
Likely benign, criteria provided, single submitter | research | National Health Laboratory Service, Universitas Academic Hospital and University of the Free State | Feb 22, 2021 | - - |
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