rs12919
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138400.2(NOM1):c.2434G>A(p.Val812Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 1,612,708 control chromosomes in the GnomAD database, including 239,928 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_138400.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOM1 | NM_138400.2 | c.2434G>A | p.Val812Met | missense_variant | 11/11 | ENST00000275820.4 | |
NOM1 | NM_001353366.2 | c.2437G>A | p.Val813Met | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOM1 | ENST00000275820.4 | c.2434G>A | p.Val812Met | missense_variant | 11/11 | 1 | NM_138400.2 | P1 | |
NOM1 | ENST00000486131.1 | n.468G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.533 AC: 80951AN: 151932Hom.: 21900 Cov.: 32
GnomAD3 exomes AF: 0.516 AC: 129185AN: 250510Hom.: 34327 AF XY: 0.515 AC XY: 69742AN XY: 135434
GnomAD4 exome AF: 0.543 AC: 793137AN: 1460658Hom.: 218020 Cov.: 42 AF XY: 0.541 AC XY: 393192AN XY: 726618
GnomAD4 genome ? AF: 0.533 AC: 80997AN: 152050Hom.: 21908 Cov.: 32 AF XY: 0.526 AC XY: 39054AN XY: 74302
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at