rs72551372
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003889.4(NR1I2):c.418G>A(p.Val140Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_003889.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR1I2 | NM_003889.4 | c.418G>A | p.Val140Met | missense_variant | 4/9 | ENST00000393716.8 | |
NR1I2 | NM_022002.3 | c.535G>A | p.Val179Met | missense_variant | 4/9 | ||
NR1I2 | NM_033013.3 | c.418G>A | p.Val140Met | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1I2 | ENST00000393716.8 | c.418G>A | p.Val140Met | missense_variant | 4/9 | 1 | NM_003889.4 | P2 | |
NR1I2 | ENST00000337940.4 | c.535G>A | p.Val179Met | missense_variant | 4/9 | 1 | A2 | ||
NR1I2 | ENST00000466380.6 | c.418G>A | p.Val140Met | missense_variant | 4/9 | 1 | A2 | ||
NR1I2 | ENST00000493757.1 | n.550G>A | non_coding_transcript_exon_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250696Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135614
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461698Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727130
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74346
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at