chr7-30431253-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.558
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
NOD1NM_006092.4 linkuse as main transcriptc.2706-1796C>G intron_variant ENST00000222823.9 NP_006083.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NOD1ENST00000222823.9 linkuse as main transcriptc.2706-1796C>G intron_variant 1 NM_006092.4 ENSP00000222823 P1Q9Y239-1
NOD1ENST00000434755.5 linkuse as main transcriptc.*416-1796C>G intron_variant, NMD_transcript_variant 2 ENSP00000416946
NOD1ENST00000467706.1 linkuse as main transcriptn.320-1796C>G intron_variant, non_coding_transcript_variant 2
NOD1ENST00000489614.5 linkuse as main transcriptn.1838-1796C>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.333
AC:
50622
AN:
151954
Hom.:
8843
Cov.:
33
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.439
Gnomad4 AMR
AF:
0.351
Gnomad4 ASJ
AF:
0.292
Gnomad4 EAS
AF:
0.261
Gnomad4 SAS
AF:
0.256
Gnomad4 FIN
AF:
0.213
Gnomad4 NFE
AF:
0.295
Gnomad4 OTH
AF:
0.309
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

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.

Other links and lift over

dbSNP: rs10267377; hg19: chr7-30470869; API