Variant chr19-53793980-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_144687.4(NLRP12):c.*69C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 1,034,734 control chromosomes in the GnomAD database, including 3,041 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.064 ( 402 hom., cov: 31)

Exomes 𝑓: 0.065 ( 2639 hom. )

Consequence

NLRP12
NM_144687.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.39

Variant links:

Genes affected

NLRP12 (HGNC:22938): (NLR family pyrin domain containing 12) This gene encodes a member of the CATERPILLER family of cytoplasmic proteins. The encoded protein, which contains an N-terminal pyrin domain, a NACHT domain, a NACHT-associated domain, and a C-terminus leucine-rich repeat region, functions as an attenuating factor of inflammation by suppressing inflammatory responses in activated monocytes. Mutations in this gene cause familial cold autoinflammatory syndrome type 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]

NLRP12 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BP6

Variant 19-53793980-G-T is Benign according to our data. Variant chr19-53793980-G-T is described in ClinVar as [Benign]. Clinvar id is 329997.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NLRP12	NM_144687.4 linkuse as main transcript	c.*69C>A		3_prime_UTR_variant	10/10	ENST00000324134.11	NP_653288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NLRP12	ENST00000324134.11 linkuse as main transcript	c.*69C>A		3_prime_UTR_variant	10/10	1	NM_144687.4	ENSP00000319377	P4	P59046-1

Frequencies

GnomAD3 genomes

AF:

0.0636

AC:

9663

AN:

151902

Hom.:

401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0717

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.0535

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.0212

Gnomad MID

AF:

0.0446

Gnomad NFE

AF:

0.0564

Gnomad OTH

AF:

0.0569

GnomAD4 exome

AF:

0.0647

AC:

57102

AN:

882714

Hom.:

2639

Cov.:

AF XY:

0.0685

AC XY:

31730

AN XY:

463526

show subpopulations

Gnomad4 AFR exome

AF:

0.0729

Gnomad4 AMR exome

AF:

0.0435

Gnomad4 ASJ exome

AF:

0.0175

Gnomad4 EAS exome

AF:

0.134

Gnomad4 SAS exome

AF:

0.159

Gnomad4 FIN exome

AF:

0.0241

Gnomad4 NFE exome

AF:

0.0552

Gnomad4 OTH exome

AF:

0.0653

GnomAD4 genome

AF:

0.0637

AC:

9688

AN:

152020

Hom.:

402

Cov.:

AF XY:

0.0638

AC XY:

4737

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.0720

Gnomad4 AMR

AF:

0.0535

Gnomad4 ASJ

AF:

0.0109

Gnomad4 EAS

AF:

0.144

Gnomad4 SAS

AF:

0.175

Gnomad4 FIN

AF:

0.0212

Gnomad4 NFE

AF:

0.0564

Gnomad4 OTH

AF:

0.0611

Alfa

AF:

0.0501

Hom.:

228

Bravo

AF:

0.0625

Asia WGS

AF:

0.212

AC:

737

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 14, 2021	- -

Familial cold autoinflammatory syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.13

DANN

Benign

0.37

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