Variant 19-54923899-TC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001127255.2(NLRP7):c.2982-28delG 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_001127255.2 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.799

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:

Genome browser will be placed here

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	Effect	Protein	UniProt
NLRP7	NM_001127255.2 linkuse as main transcript	c.2982-28delG	intron_variant	NP_001120727.1	Q8WX94-3
NLRP7	NM_001405531.1 linkuse as main transcript	c.2982-28delG	intron_variant	NP_001392460.1
NLRP7	NM_139176.4 linkuse as main transcript	c.2898-28delG	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.2982-28delG		intron_variant		1		ENSP00000468706.1		Q8WX94-3

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17997

AN:

152030

Hom.:

1356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.0403

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.0592

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0753

Gnomad OTH

AF:

0.122

GnomAD3 exomes

AF:

0.123

AC:

30541

AN:

248580

Hom.:

2725

AF XY:

0.113

AC XY:

15213

AN XY:

134680

show subpopulations

Gnomad AFR exome

AF:

0.151

Gnomad AMR exome

AF:

0.212

Gnomad ASJ exome

AF:

0.0382

Gnomad EAS exome

AF:

0.310

Gnomad SAS exome

AF:

0.0486

Gnomad FIN exome

AF:

0.187

Gnomad NFE exome

AF:

0.0769

Gnomad OTH exome

AF:

0.105

GnomAD4 exome

AF:

0.0879

AC:

128243

AN:

1459464

Hom.:

7730

Cov.:

AF XY:

0.0855

AC XY:

62092

AN XY:

726178

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.209

Gnomad4 ASJ exome

AF:

0.0384

Gnomad4 EAS exome

AF:

0.301

Gnomad4 SAS exome

AF:

0.0472

Gnomad4 FIN exome

AF:

0.180

Gnomad4 NFE exome

AF:

0.0733

Gnomad4 OTH exome

AF:

0.0957

GnomAD4 genome

AF:

0.119

AC:

18038

AN:

152148

Hom.:

1363

Cov.:

AF XY:

0.124

AC XY:

9224

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.146

Gnomad4 AMR

AF:

0.159

Gnomad4 ASJ

AF:

0.0403

Gnomad4 EAS

AF:

0.318

Gnomad4 SAS

AF:

0.0589

Gnomad4 FIN

AF:

0.194

Gnomad4 NFE

AF:

0.0753

Gnomad4 OTH

AF:

0.124

Alfa

AF:

0.0851

Hom.:

106

Bravo

AF:

0.121

Asia WGS

AF:

0.192

AC:

670

AN:

3478

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

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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