rs269951

chr19-54930627-A-Gchr19-54930627-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001405531.1(NLRP7):c.2682T>C(p.Tyr894=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 1,610,306 control chromosomes in the GnomAD database, including 255,126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.55 (23580 hom., cov: 31)
  • Exomes 𝑓: 0.56 (231546 hom.)
• Consequence: NLRP7 NM_001405531.1 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -0.264

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]

NCR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BP6: Variant 19-54930627-A-G is Benign according to our data. Variant chr19-54930627-A-G is described in ClinVar as [Benign]. Clinvar id is 330158.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-54930627-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NLRP7	NM_001127255.2	c.2682T>C	p.Tyr894=	synonymous_variant	9/11	ENST00000592784.6
NLRP7	NM_001405531.1	c.2682T>C	p.Tyr894=	synonymous_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NLRP7	ENST00000592784.6	c.2682T>C	p.Tyr894=	synonymous_variant	9/11	1	NM_001127255.2	P2

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84139 AN: 151824 Hom.: 23559 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.552

GnomAD3 exomes AF: 0.588 AC: 147809 AN: 251440 Hom.: 44097 AF XY: 0.589 AC XY: 80048 AN XY: 135896

Gnomad AFR exome AF: 0.519

Gnomad AMR exome AF: 0.645

Gnomad ASJ exome AF: 0.628

Gnomad EAS exome AF: 0.716

Gnomad SAS exome AF: 0.630

Gnomad FIN exome AF: 0.553

Gnomad NFE exome AF: 0.553

Gnomad OTH exome AF: 0.566

GnomAD4 exome AF: 0.561 AC: 818657 AN: 1458364 Hom.: 231546 Cov.: 34 AF XY: 0.565 AC XY: 409847 AN XY: 725660

Gnomad4 AFR exome AF: 0.511

Gnomad4 AMR exome AF: 0.639

Gnomad4 ASJ exome AF: 0.627

Gnomad4 EAS exome AF: 0.719

Gnomad4 SAS exome AF: 0.637

Gnomad4 FIN exome AF: 0.550

Gnomad4 NFE exome AF: 0.546

Gnomad4 OTH exome AF: 0.573

GnomAD4 genome AF: 0.554 AC: 84203 AN: 151942 Hom.: 23580 Cov.: 31 AF XY: 0.557 AC XY: 41388 AN XY: 74254

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.550

Alfa AF: 0.556 Hom.: 24813

Bravo AF: 0.553

Asia WGS AF: 0.619 AC: 2154 AN: 3478

EpiCase AF: 0.555

EpiControl AF: 0.552

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hydatidiform mole, recurrent, 1 Benign:3

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 10, 2014	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.23
Dann	Benign	0.27

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

Other links and lift over

dbSNP: rs269951; hg19: chr19-55441995; COSMIC: COSV60172236;