Variant 7-30456766-G-C 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.156C>G(p.Ala52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,613,648 control chromosomes in the GnomAD database, including 61,307 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. Synonymous variant affecting the same amino acid position (i.e. A52A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.32 ( 8521 hom., cov: 32)

Exomes 𝑓: 0.26 ( 52786 hom. )

Consequence

NOD1
NM_006092.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.35

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:

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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=-0.85).

BP7

Synonymous conserved (PhyloP=-3.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOD1	NM_006092.4 linkuse as main transcript	c.156C>G	p.Ala52=	synonymous_variant	4/14	ENST00000222823.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOD1	ENST00000222823.9 linkuse as main transcript	c.156C>G	p.Ala52=	synonymous_variant	4/14	1	NM_006092.4	P1	Q9Y239-1

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

47922

AN:

151792

Hom.:

8512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.476

Gnomad AMI

AF:

0.131

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.328

GnomAD3 exomes

AF:

0.279

AC:

70221

AN:

251374

Hom.:

10782

AF XY:

0.283

AC XY:

38451

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.486

Gnomad AMR exome

AF:

0.152

Gnomad ASJ exome

AF:

0.249

Gnomad EAS exome

AF:

0.349

Gnomad SAS exome

AF:

0.379

Gnomad FIN exome

AF:

0.282

Gnomad NFE exome

AF:

0.253

Gnomad OTH exome

AF:

0.270

GnomAD4 exome

AF:

0.262

AC:

382399

AN:

1461738

Hom.:

52786

Cov.:

AF XY:

0.265

AC XY:

192759

AN XY:

727186

show subpopulations

Gnomad4 AFR exome

AF:

0.483

Gnomad4 AMR exome

AF:

0.160

Gnomad4 ASJ exome

AF:

0.248

Gnomad4 EAS exome

AF:

0.413

Gnomad4 SAS exome

AF:

0.378

Gnomad4 FIN exome

AF:

0.282

Gnomad4 NFE exome

AF:

0.243

Gnomad4 OTH exome

AF:

0.279

GnomAD4 genome

AF:

0.316

AC:

47959

AN:

151910

Hom.:

8521

Cov.:

AF XY:

0.318

AC XY:

23639

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.475

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.237

Gnomad4 EAS

AF:

0.366

Gnomad4 SAS

AF:

0.386

Gnomad4 FIN

AF:

0.278

Gnomad4 NFE

AF:

0.247

Gnomad4 OTH

AF:

0.327

Alfa

AF:

0.224

Hom.:

1346

Bravo

AF:

0.317

Asia WGS

AF:

0.371

AC:

1287

AN:

3478

EpiCase

AF:

0.255

EpiControl

AF:

0.259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.040

DANN

Benign

0.37

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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