Genetic Variant NOD2:c.2885+64A>T (chr16-50725636-A-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001370466.1(NOD2):c.2885+64A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 1,297,068 control chromosomes in the GnomAD database, including 240,148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.51 ( 22312 hom., cov: 31)

Exomes 𝑓: 0.60 ( 217836 hom. )

Consequence

NOD2
NM_001370466.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.44

Variant links:

Genes affected

NOD2 (HGNC:5331): (nucleotide binding oligomerization domain containing 2) This gene is a member of the Nod1/Apaf-1 family and encodes a protein with two caspase recruitment (CARD) domains and six leucine-rich repeats (LRRs). The protein is primarily expressed in the peripheral blood leukocytes. It plays a role in the immune response to intracellular bacterial lipopolysaccharides (LPS) by recognizing the muramyl dipeptide (MDP) derived from them and activating the NFKB protein. Mutations in this gene have been associated with Crohn disease and Blau syndrome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jun 2014]

NOD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 16-50725636-A-T is Benign according to our data. Variant chr16-50725636-A-T is described in ClinVar as [Benign]. Clinvar id is 2628170.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOD2	NM_001370466.1 link	c.2885+64A>T		intron_variant	Intron 10 of 11	ENST00000647318.2	NP_001357395.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOD2	ENST00000647318.2 link	c.2885+64A>T		intron_variant	Intron 10 of 11		NM_001370466.1	ENSP00000495993.1		Q9HC29-2

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77301

AN:

151924

Hom.:

22315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.809

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.764

Gnomad EAS

AF:

0.152

Gnomad SAS

AF:

0.346

Gnomad FIN

AF:

0.566

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.662

Gnomad OTH

AF:

0.547

GnomAD4 exome

AF:

0.602

AC:

688886

AN:

1145026

Hom.:

217836

AF XY:

0.597

AC XY:

349311

AN XY:

584652

show subpopulations

Gnomad4 AFR exome

AF:

0.272

Gnomad4 AMR exome

AF:

0.417

Gnomad4 ASJ exome

AF:

0.774

Gnomad4 EAS exome

AF:

0.177

Gnomad4 SAS exome

AF:

0.392

Gnomad4 FIN exome

AF:

0.568

Gnomad4 NFE exome

AF:

0.661

Gnomad4 OTH exome

AF:

0.574

GnomAD4 genome

AF:

0.509

AC:

77318

AN:

152042

Hom.:

22312

Cov.:

AF XY:

0.501

AC XY:

37239

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.275

Gnomad4 AMR

AF:

0.511

Gnomad4 ASJ

AF:

0.764

Gnomad4 EAS

AF:

0.152

Gnomad4 SAS

AF:

0.346

Gnomad4 FIN

AF:

0.566

Gnomad4 NFE

AF:

0.662

Gnomad4 OTH

AF:

0.543

Alfa

AF:

0.569

Hom.:

3327

Bravo

AF:

0.492

Asia WGS

AF:

0.260

AC:

907

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Nov 12, 2023

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 51% of patients studied by a panel of primary immunodeficiencies. Number of patients: 49. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.012

DANN

Benign

0.43

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