7-30431253-G-C

Variant names:

• chr7-30431253-G-C
• rs10267377
• NM_006092.4:c.2706-1796C>G

Variant summary

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

The NM_006092.4(NOD1):​c.2706-1796C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,074 control chromosomes in the GnomAD database, including 8,870 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 0.33 (8870 hom., cov: 33)
• Consequence: NOD1 NM_006092.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 8 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOD1	NM_006092.4	c.2706-1796C>G		intron_variant	Intron 12 of 13	ENST00000222823.9	NP_006083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOD1	ENST00000222823.9	c.2706-1796C>G		intron_variant	Intron 12 of 13	1	NM_006092.4	ENSP00000222823.4
NOD1	ENST00000434755.5	n.*416-1796C>G		intron_variant	Intron 12 of 14	2		ENSP00000416946.1
NOD1	ENST00000467706.1	n.320-1796C>G		intron_variant	Intron 1 of 2	2
NOD1	ENST00000489614.5	n.1838-1796C>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50622 AN: 151954 Hom.: 8843 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.333 AC: 50686 AN: 152074 Hom.: 8870 Cov.: 33 AF XY: 0.328 AC XY: 24355 AN XY: 74318

African (AFR) AF: 0.439 AC: 18206 AN: 41460

American (AMR) AF: 0.351 AC: 5360 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1011 AN: 3466

East Asian (EAS) AF: 0.261 AC: 1351 AN: 5180

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4826

European-Finnish (FIN) AF: 0.213 AC: 2253 AN: 10580

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20077 AN: 67964

Other (OTH) AF: 0.309 AC: 649 AN: 2102

Alfa AF: 0.303 Hom.: 877

Bravo AF: 0.350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.56
PhyloP100		-0.56
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: rs10267377; hg19: chr7-30470869;