Variant rs2235099 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006092.4(NOD1):c.483C>T(p.Asp161Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,613,624 control chromosomes in the GnomAD database, including 57,135 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 0.28 ( 6561 hom., cov: 32)

Exomes 𝑓: 0.26 ( 50574 hom. )

Consequence

NOD1
NM_006092.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.83

Variant links:

Genes affected

NOD1 (HGNC:16390): (nucleotide binding oligomerization domain containing 1) This gene encodes a member of the nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) family of proteins. The encoded protein plays a role in innate immunity by acting as a pattern-recognition receptor (PRR) that binds bacterial peptidoglycans and initiates inflammation. This protein has also been implicated in the immune response to viral and parasitic infection. Major structural features of this protein include an N-terminal caspase recruitment domain (CARD), a centrally located nucleotide-binding domain (NBD), and 10 tandem leucine-rich repeats (LRRs) in its C terminus. The CARD is involved in apoptotic signaling, LRRs participate in protein-protein interactions, and mutations in the NBD may affect the process of oligomerization and subsequent function of the LRR domain. Mutations in this gene are associated with asthma, inflammatory bowel disease, Behcet disease and sarcoidosis in human patients. [provided by RefSeq, Aug 2017]

NOD1 links:

NOD1 (HGNC:):

NOD1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP7

Synonymous conserved (PhyloP=1.83 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOD1	NM_006092.4 linkuse as main transcript	c.483C>T	p.Asp161Asp	synonymous_variant	6/14	ENST00000222823.9	NP_006083.1	Q9Y239-1A0A024RA73

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOD1	ENST00000222823.9 linkuse as main transcript	c.483C>T	p.Asp161Asp	synonymous_variant	6/14	1	NM_006092.4	ENSP00000222823.4		Q9Y239-1
NOD1	ENST00000434755.5 linkuse as main transcript	n.483C>T		non_coding_transcript_exon_variant	6/15	2		ENSP00000416946.1		G3XAL1

Frequencies

GnomAD3 genomes

AF:

0.284

AC:

43152

AN:

151854

Hom.:

6555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.369

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.385

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.302

GnomAD3 exomes

AF:

0.271

AC:

67827

AN:

250654

Hom.:

9927

AF XY:

0.276

AC XY:

37460

AN XY:

135512

show subpopulations

Gnomad AFR exome

AF:

0.378

Gnomad AMR exome

AF:

0.146

Gnomad ASJ exome

AF:

0.249

Gnomad EAS exome

AF:

0.350

Gnomad SAS exome

AF:

0.379

Gnomad FIN exome

AF:

0.280

Gnomad NFE exome

AF:

0.252

Gnomad OTH exome

AF:

0.263

GnomAD4 exome

AF:

0.257

AC:

376322

AN:

1461652

Hom.:

50574

Cov.:

AF XY:

0.261

AC XY:

190041

AN XY:

727126

show subpopulations

Gnomad4 AFR exome

AF:

0.373

Gnomad4 AMR exome

AF:

0.153

Gnomad4 ASJ exome

AF:

0.247

Gnomad4 EAS exome

AF:

0.412

Gnomad4 SAS exome

AF:

0.378

Gnomad4 FIN exome

AF:

0.279

Gnomad4 NFE exome

AF:

0.242

Gnomad4 OTH exome

AF:

0.269

GnomAD4 genome

AF:

0.284

AC:

43182

AN:

151972

Hom.:

6561

Cov.:

AF XY:

0.286

AC XY:

21271

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.369

Gnomad4 AMR

AF:

0.191

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.387

Gnomad4 FIN

AF:

0.277

Gnomad4 NFE

AF:

0.245

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.260

Hom.:

2948

Bravo

AF:

0.281

Asia WGS

AF:

0.370

AC:

1282

AN:

3478

EpiCase

AF:

0.253

EpiControl

AF:

0.257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

8.0

DANN

Benign

0.38

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over