rs2276707
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003889.4(NR1I2):c.938-17C>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,605,722 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.938-17C>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000393716.8 | |||
NR1I2 | NM_022002.3 | c.1055-17C>G | splice_polypyrimidine_tract_variant, intron_variant | ||||
NR1I2 | NM_033013.3 | c.827-17C>G | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1I2 | ENST00000393716.8 | c.938-17C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003889.4 | P2 | |||
NR1I2 | ENST00000337940.4 | c.1055-17C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
NR1I2 | ENST00000466380.6 | c.827-17C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
NR1I2 | ENST00000493757.1 | n.1070-17C>G | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00168 AC: 255AN: 151984Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000414 AC: 104AN: 251252Hom.: 0 AF XY: 0.000361 AC XY: 49AN XY: 135824
GnomAD4 exome AF: 0.000129 AC: 188AN: 1453620Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 68AN XY: 723750
GnomAD4 genome ? AF: 0.00168 AC: 255AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.00160 AC XY: 119AN XY: 74334
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at