Genetic Variant NM_176810.2:c.2619-85C>T (chr19-55902290-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_176810.2(NLRP13):c.2619-85C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000573 in 1,082,038 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.000087 ( 0 hom., cov: 27)

Exomes 𝑓: 0.000054 ( 1 hom. )

Consequence

NLRP13
NM_176810.2 intron

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -0.744

Publications

0 publications found

Variant links:

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]

NLRP13 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NLRP13	NM_176810.2 link	c.2619-85C>T		intron_variant	Intron 8 of 10	ENST00000342929.4	NP_789780.2
NLRP13	NM_001321057.1 link	c.2619-85C>T		intron_variant	Intron 8 of 11		NP_001307986.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NLRP13	ENST00000342929.4 link	c.2619-85C>T		intron_variant	Intron 8 of 10	1	NM_176810.2	ENSP00000343891.3		Q86W25
NLRP13	ENST00000588751.5 link	c.2619-85C>T		intron_variant	Intron 8 of 11	5		ENSP00000467899.1		A0A0C4DGQ4

Frequencies

GnomAD3 genomes

AF:

0.0000775

AC:

AN:

103240

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000371

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000192

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000281

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000866

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000542

AC:

AN:

978668

Hom.:

AF XY:

0.0000387

AC XY:

AN XY:

490394

show subpopulations

African (AFR)

AF:

0.000349

AC:

AN:

22942

American (AMR)

AF:

0.000299

AC:

AN:

26740

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18020

East Asian (EAS)

AF:

0.000122

AC:

AN:

32758

South Asian (SAS)

AF:

0.00

AC:

AN:

54886

European-Finnish (FIN)

AF:

0.00

AC:

AN:

37942

Middle Eastern (MID)

AF:

0.000928

AC:

AN:

3234

European-Non Finnish (NFE)

AF:

0.0000406

AC:

AN:

739692

Other (OTH)

AF:

0.00

AC:

AN:

42454

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.549

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000871

AC:

AN:

103370

Hom.:

Cov.:

AF XY:

0.000136

AC XY:

AN XY:

51320

show subpopulations

African (AFR)

AF:

0.0000738

AC:

AN:

27094

American (AMR)

AF:

0.000192

AC:

AN:

10410

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2398

East Asian (EAS)

AF:

0.000282

AC:

AN:

3546

South Asian (SAS)

AF:

0.00

AC:

AN:

3236

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8396

Middle Eastern (MID)

AF:

0.00

AC:

AN:

152

European-Non Finnish (NFE)

AF:

0.0000866

AC:

AN:

46194

Other (OTH)

AF:

0.00

AC:

AN:

1342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.000142

Hom.:

Bravo

AF:

0.0000642

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not provided

Other:1

Human Evolutionary Genetics, Institut Pasteur

Significance:not provided

Review Status:no classification provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.94

(source)

DANN

Benign

0.42

PhyloP100

-0.74

Mutation Taster

=100/0

polymorphism

(source)

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

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NM_176810.2:c.2619-85C>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over