rs104895419
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001370466.1(NOD2):c.234G>A(p.Ala78=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. A78A) has been classified as Likely benign.
Frequency
Consequence
NM_001370466.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOD2 | NM_001370466.1 | c.234G>A | p.Ala78= | synonymous_variant | 2/12 | ENST00000647318.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOD2 | ENST00000647318.2 | c.234G>A | p.Ala78= | synonymous_variant | 2/12 | NM_001370466.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250822Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135706
GnomAD4 exome AF: 0.000136 AC: 199AN: 1461824Hom.: 0 Cov.: 33 AF XY: 0.000127 AC XY: 92AN XY: 727208
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74334
ClinVar
Submissions by phenotype
Regional enteritis;C5201146:Blau syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Blau syndrome Other:1
not provided, no classification provided | literature only | Unité médicale des maladies autoinflammatoires, CHRU Montpellier | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at