3-119807374-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_003889.4(NR1I2):c.124C>T(p.Arg42Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003889.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR1I2 | NM_003889.4 | c.124C>T | p.Arg42Cys | missense_variant | Exon 2 of 9 | ENST00000393716.8 | NP_003880.3 | |
NR1I2 | NM_022002.3 | c.241C>T | p.Arg81Cys | missense_variant | Exon 2 of 9 | NP_071285.1 | ||
NR1I2 | NM_033013.3 | c.124C>T | p.Arg42Cys | missense_variant | Exon 2 of 9 | NP_148934.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251466Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135904
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461864Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727230
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.124C>T (p.R42C) alteration is located in exon 2 (coding exon 1) of the NR1I2 gene. This alteration results from a C to T substitution at nucleotide position 124, causing the arginine (R) at amino acid position 42 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at