NM_176810.2:c.320-3037C>T

Variant names:

• chr19-55928072-G-A
• rs382958
• NM_176810.2:c.320-3037C>T

Variant summary

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

The NM_176810.2(NLRP13):​c.320-3037C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,936 control chromosomes in the GnomAD database, including 28,148 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 0.60 (28148 hom., cov: 31)
• Consequence: NLRP13 NM_176810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 publications found

Genes affected

NLRP13 (HGNC:22937): (NLR family pyrin domain containing 13) 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. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_176810.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLRP13	NM_176810.2	MANE Select	c.320-3037C>T		intron	N/A	NP_789780.2
	NLRP13	NM_001321057.1		c.320-3037C>T		intron	N/A	NP_001307986.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NLRP13	ENST00000342929.4	TSL:1 MANE Select	c.320-3037C>T		intron	N/A	ENSP00000343891.3
	NLRP13	ENST00000588751.5	TSL:5	c.320-3037C>T		intron	N/A	ENSP00000467899.1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91811 AN: 151818 Hom.: 28130 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.605 AC: 91876 AN: 151936 Hom.: 28148 Cov.: 31 AF XY: 0.611 AC XY: 45399 AN XY: 74254

African (AFR) AF: 0.611 AC: 25331 AN: 41434

American (AMR) AF: 0.679 AC: 10366 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2095 AN: 3464

East Asian (EAS) AF: 0.834 AC: 4293 AN: 5150

South Asian (SAS) AF: 0.664 AC: 3202 AN: 4824

European-Finnish (FIN) AF: 0.646 AC: 6790 AN: 10514

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37873 AN: 67966

Other (OTH) AF: 0.610 AC: 1286 AN: 2108

Alfa AF: 0.575 Hom.: 13971

Bravo AF: 0.606

Asia WGS AF: 0.743 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.21
PhyloP100		-1.5
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: rs382958; hg19: chr19-56439438;