chr3-119812953-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_003889.4(NR1I2):c.787T>C(p.Tyr263His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,292 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y263C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003889.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR1I2 | NM_003889.4 | c.787T>C | p.Tyr263His | missense_variant | 5/9 | ENST00000393716.8 | |
NR1I2 | NM_022002.3 | c.904T>C | p.Tyr302His | missense_variant | 5/9 | ||
NR1I2 | NM_033013.3 | c.676T>C | p.Tyr226His | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1I2 | ENST00000393716.8 | c.787T>C | p.Tyr263His | missense_variant | 5/9 | 1 | NM_003889.4 | P2 | |
NR1I2 | ENST00000337940.4 | c.904T>C | p.Tyr302His | missense_variant | 5/9 | 1 | A2 | ||
NR1I2 | ENST00000466380.6 | c.676T>C | p.Tyr226His | missense_variant | 5/9 | 1 | A2 | ||
NR1I2 | ENST00000493757.1 | n.919T>C | non_coding_transcript_exon_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247174Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133844
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461036Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 726802
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74392
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at