Variant 19-54927572-AAAAC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001127255.2(NLRP7):c.2981+29_2981+32delGTTT 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: 𝑓 0.55 ( 23404 hom., cov: 0)

Exomes 𝑓: 0.56 ( 230375 hom. )

Consequence

NLRP7
NM_001127255.2 intron

Scores

Not classified

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 0.260

Variant links:

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]

NLRP7 links:

NCR1 (HGNC:6731): (natural cytotoxicity triggering receptor 1) Predicted to be involved in cellular defense response; regulation of natural killer cell mediated cytotoxicity; and signal transduction. Predicted to act upstream of or within defense response to virus and detection of virus. Predicted to be located in cell surface. Predicted to be part of SWI/SNF complex. Predicted to be active in plasma membrane. Biomarker of acquired immunodeficiency syndrome; anogenital venereal wart; hepatitis C; and lymphoproliferative syndrome. [provided by Alliance of Genome Resources, Apr 2022]

NCR1 links:

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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	Effect	Protein	UniProt
NLRP7	NM_001127255.2 linkuse as main transcript	c.2981+29_2981+32delGTTT	intron_variant	NP_001120727.1	Q8WX94-3
NLRP7	NM_001405531.1 linkuse as main transcript	c.2981+29_2981+32delGTTT	intron_variant	NP_001392460.1
NLRP7	NM_139176.4 linkuse as main transcript	c.2897+29_2897+32delGTTT	intron_variant	NP_631915.2	Q8WX94-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NLRP7	ENST00000592784.6 linkuse as main transcript	c.2981+29_2981+32delGTTT		intron_variant		1		ENSP00000468706.1		Q8WX94-3

Frequencies

GnomAD3 genomes

AF:

0.554

AC:

83739

AN:

151210

Hom.:

23382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.521

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.578

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.711

Gnomad SAS

AF:

0.629

Gnomad FIN

AF:

0.549

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.552

Gnomad OTH

AF:

0.549

GnomAD3 exomes

AF:

0.586

AC:

145854

AN:

248942

Hom.:

43313

AF XY:

0.586

AC XY:

79109

AN XY:

134930

show subpopulations

Gnomad AFR exome

AF:

0.523

Gnomad AMR exome

AF:

0.644

Gnomad ASJ exome

AF:

0.620

Gnomad EAS exome

AF:

0.714

Gnomad SAS exome

AF:

0.617

Gnomad FIN exome

AF:

0.553

Gnomad NFE exome

AF:

0.552

Gnomad OTH exome

AF:

0.562

GnomAD4 exome

AF:

0.560

AC:

815566

AN:

1456626

Hom.:

230375

AF XY:

0.563

AC XY:

408197

AN XY:

724760

show subpopulations

Gnomad4 AFR exome

AF:

0.514

Gnomad4 AMR exome

AF:

0.638

Gnomad4 ASJ exome

AF:

0.621

Gnomad4 EAS exome

AF:

0.719

Gnomad4 SAS exome

AF:

0.630

Gnomad4 FIN exome

AF:

0.549

Gnomad4 NFE exome

AF:

0.545

Gnomad4 OTH exome

AF:

0.572

GnomAD4 genome

AF:

0.554

AC:

83805

AN:

151330

Hom.:

23404

Cov.:

AF XY:

0.557

AC XY:

41140

AN XY:

73880

show subpopulations

Gnomad4 AFR

AF:

0.521

Gnomad4 AMR

AF:

0.579

Gnomad4 ASJ

AF:

0.618

Gnomad4 EAS

AF:

0.712

Gnomad4 SAS

AF:

0.629

Gnomad4 FIN

AF:

0.549

Gnomad4 NFE

AF:

0.552

Gnomad4 OTH

AF:

0.547

Alfa

AF:

0.528

Hom.:

2072

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over