Variant 19-54927800-C-G details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: -0.186

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:):

NCR1 links:

Genome browser will be placed here

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 linkuse as main transcript	c.2811-25G>C		intron_variant		ENST00000592784.6
NLRP7	NM_001405531.1 linkuse as main transcript	c.2811-25G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NLRP7	ENST00000592784.6 linkuse as main transcript	c.2811-25G>C		intron_variant		1	NM_001127255.2	P2	Q8WX94-3

Frequencies

GnomAD3 genomes

AF:

0.0597

AC:

9073

AN:

152036

Hom.:

627

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0886

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.00851

Gnomad FIN

AF:

0.0141

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00247

Gnomad OTH

AF:

0.0575

GnomAD3 exomes

AF:

0.0386

AC:

9704

AN:

251258

Hom.:

587

AF XY:

0.0303

AC XY:

4118

AN XY:

135804

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.116

Gnomad ASJ exome

AF:

0.00268

Gnomad EAS exome

AF:

0.114

Gnomad SAS exome

AF:

0.00356

Gnomad FIN exome

AF:

0.0146

Gnomad NFE exome

AF:

0.00260

Gnomad OTH exome

AF:

0.0264

GnomAD4 exome

AF:

0.0126

AC:

18381

AN:

1453650

Hom.:

1047

Cov.:

AF XY:

0.0114

AC XY:

8217

AN XY:

723842

show subpopulations

Gnomad4 AFR exome

AF:

0.168

Gnomad4 AMR exome

AF:

0.111

Gnomad4 ASJ exome

AF:

0.00219

Gnomad4 EAS exome

AF:

0.0920

Gnomad4 SAS exome

AF:

0.00418

Gnomad4 FIN exome

AF:

0.0150

Gnomad4 NFE exome

AF:

0.00128

Gnomad4 OTH exome

AF:

0.0242

GnomAD4 genome

AF:

0.0599

AC:

9108

AN:

152154

Hom.:

627

Cov.:

AF XY:

0.0600

AC XY:

4467

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.0889

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.112

Gnomad4 SAS

AF:

0.00810

Gnomad4 FIN

AF:

0.0141

Gnomad4 NFE

AF:

0.00247

Gnomad4 OTH

AF:

0.0583

Alfa

AF:

0.0104

Hom.:

Bravo

AF:

0.0708

Asia WGS

AF:

0.0660

AC:

231

AN:

3478

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

Cadd

Benign

2.0

Dann

Benign

0.36

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