chr19-54927800-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001405531.1(NLRP7):c.2811-25G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0171 in 1,605,804 control chromosomes in the GnomAD database, including 1,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.060 ( 627 hom., cov: 33)
Exomes 𝑓: 0.013 ( 1047 hom. )
Consequence
NLRP7
NM_001405531.1 intron
NM_001405531.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.186
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 19-54927800-C-G is Benign according to our data. Variant chr19-54927800-C-G is described in ClinVar as [Benign]. Clinvar id is 97770.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP7 | NM_001127255.2 | c.2811-25G>C | intron_variant | ENST00000592784.6 | |||
NLRP7 | NM_001405531.1 | c.2811-25G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP7 | ENST00000592784.6 | c.2811-25G>C | intron_variant | 1 | NM_001127255.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0597 AC: 9073AN: 152036Hom.: 627 Cov.: 33
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GnomAD3 exomes AF: 0.0386 AC: 9704AN: 251258Hom.: 587 AF XY: 0.0303 AC XY: 4118AN XY: 135804
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GnomAD4 exome AF: 0.0126 AC: 18381AN: 1453650Hom.: 1047 Cov.: 32 AF XY: 0.0114 AC XY: 8217AN XY: 723842
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GnomAD4 genome ? AF: 0.0599 AC: 9108AN: 152154Hom.: 627 Cov.: 33 AF XY: 0.0600 AC XY: 4467AN XY: 74428
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hydatidiform mole Benign:1
Benign, criteria provided, single submitter | research | National Health Laboratory Service, Universitas Academic Hospital and University of the Free State | Feb 22, 2021 | - - |
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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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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