7-30452621-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006092.4(NOD1):c.796G>A(p.Glu266Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,613,520 control chromosomes in the GnomAD database, including 56,779 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006092.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOD1 | NM_006092.4 | c.796G>A | p.Glu266Lys | missense_variant | 6/14 | ENST00000222823.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOD1 | ENST00000222823.9 | c.796G>A | p.Glu266Lys | missense_variant | 6/14 | 1 | NM_006092.4 | P1 | |
NOD1 | ENST00000434755.5 | c.796G>A | p.Glu266Lys | missense_variant, NMD_transcript_variant | 6/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.284 AC: 43166AN: 152106Hom.: 6549 Cov.: 33
GnomAD3 exomes AF: 0.269 AC: 67586AN: 250900Hom.: 9839 AF XY: 0.275 AC XY: 37343AN XY: 135740
GnomAD4 exome AF: 0.257 AC: 375056AN: 1461296Hom.: 50224 Cov.: 38 AF XY: 0.261 AC XY: 189383AN XY: 726966
GnomAD4 genome AF: 0.284 AC: 43195AN: 152224Hom.: 6555 Cov.: 33 AF XY: 0.286 AC XY: 21291AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 14, 2021 | This variant is associated with the following publications: (PMID: 17309748, 19538217, 19882212) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at