3-119807302-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003889.4(NR1I2):c.52G>A(p.Glu18Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000769 in 1,614,242 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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 the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_003889.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR1I2 | NM_003889.4 | c.52G>A | p.Glu18Lys | missense_variant | Exon 2 of 9 | ENST00000393716.8 | NP_003880.3 | |
NR1I2 | NM_022002.3 | c.169G>A | p.Glu57Lys | missense_variant | Exon 2 of 9 | NP_071285.1 | ||
NR1I2 | NM_033013.3 | c.52G>A | p.Glu18Lys | missense_variant | Exon 2 of 9 | NP_148934.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00414 AC: 630AN: 152234Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00109 AC: 273AN: 251484Hom.: 2 AF XY: 0.000765 AC XY: 104AN XY: 135922
GnomAD4 exome AF: 0.000419 AC: 612AN: 1461890Hom.: 5 Cov.: 32 AF XY: 0.000371 AC XY: 270AN XY: 727246
GnomAD4 genome AF: 0.00414 AC: 630AN: 152352Hom.: 4 Cov.: 32 AF XY: 0.00380 AC XY: 283AN XY: 74500
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at