chr3-119812954-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003889.4(NR1I2):āc.788A>Gā(p.Tyr263Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y263H) has been classified as Likely benign.
Frequency
Consequence
NM_003889.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.788A>G | p.Tyr263Cys | missense_variant | 5/9 | ENST00000393716.8 | |
NR1I2 | NM_022002.3 | c.905A>G | p.Tyr302Cys | missense_variant | 5/9 | ||
NR1I2 | NM_033013.3 | c.677A>G | p.Tyr226Cys | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1I2 | ENST00000393716.8 | c.788A>G | p.Tyr263Cys | missense_variant | 5/9 | 1 | NM_003889.4 | P2 | |
NR1I2 | ENST00000337940.4 | c.905A>G | p.Tyr302Cys | missense_variant | 5/9 | 1 | A2 | ||
NR1I2 | ENST00000466380.6 | c.677A>G | p.Tyr226Cys | missense_variant | 5/9 | 1 | A2 | ||
NR1I2 | ENST00000493757.1 | n.920A>G | non_coding_transcript_exon_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247126Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133808
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461032Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726796
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2022 | The c.788A>G (p.Y263C) alteration is located in exon 5 (coding exon 4) of the NR1I2 gene. This alteration results from a A to G substitution at nucleotide position 788, causing the tyrosine (Y) at amino acid position 263 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