19-55828685-C-T

Variant names:

• chr19-55828685-C-T
• rs16986667
• NM_001394894.2:c.-63+3278G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394894.2(NLRP11):​c.-63+3278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,196 control chromosomes in the GnomAD database, including 856 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.087 (856 hom., cov: 32)
• Consequence: NLRP11 NM_001394894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724
• Publications: 3 publications found

Genes affected

NLRP11 (HGNC:22945): (NLR family pyrin domain containing 11) This gene is a member of the the NOD-like receptor protein (NLRP) gene family and encodes a protein with an N-terminal pyrin death (PYD) domain and nucleoside triphosphate hydrolase (NACHT) domain and a C-terminal leucine-rich repeats (LRR) region. This gene has been shown to regulate caspases in the proinflammatory signal transduction pathway and, based on studies of other members of the NLRP gene family with similar domain structure, is predicted to form part of the multiprotein inflammasome complex. Alternative splicing produces multiple transcript variants encoding distince isoforms. [provided by RefSeq, May 2017]

NLRP11 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NLRP11	NM_001394894.2	c.-63+3278G>A		intron_variant	Intron 1 of 9	ENST00000589093.6	NP_001381823.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NLRP11	ENST00000589093.6	c.-63+3278G>A		intron_variant	Intron 1 of 9	1	NM_001394894.2	ENSP00000466285.1

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13261 AN: 152076 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.0344

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.0879

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0873 AC: 13280 AN: 152196 Hom.: 856 Cov.: 32 AF XY: 0.0875 AC XY: 6506 AN XY: 74394

African (AFR) AF: 0.150 AC: 6234 AN: 41514

American (AMR) AF: 0.128 AC: 1963 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3464

East Asian (EAS) AF: 0.232 AC: 1197 AN: 5162

South Asian (SAS) AF: 0.0358 AC: 173 AN: 4828

European-Finnish (FIN) AF: 0.0344 AC: 364 AN: 10582

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2754 AN: 68024

Other (OTH) AF: 0.0874 AC: 185 AN: 2116

Alfa AF: 0.0589 Hom.: 667

Bravo AF: 0.0981

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.42
PhyloP100		0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16986667; hg19: chr19-56340051;