rs1790752
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003952.3(RPS6KB2):c.1156-9G>A 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 0.433 in 1,596,636 control chromosomes in the GnomAD database, including 156,498 homozygotes. 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_003952.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KB2 | NM_003952.3 | c.1156-9G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000312629.10 | |||
RPS6KB2 | XM_006718656.4 | c.556-9G>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KB2 | ENST00000312629.10 | c.1156-9G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003952.3 | P1 | |||
RPS6KB2-AS1 | ENST00000535922.1 | n.343+484C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.503 AC: 76435AN: 151934Hom.: 21058 Cov.: 33
GnomAD3 exomes AF: 0.424 AC: 95196AN: 224608Hom.: 21835 AF XY: 0.407 AC XY: 50188AN XY: 123364
GnomAD4 exome AF: 0.426 AC: 615308AN: 1444584Hom.: 135413 Cov.: 32 AF XY: 0.418 AC XY: 300371AN XY: 718308
GnomAD4 genome AF: 0.503 AC: 76505AN: 152052Hom.: 21085 Cov.: 33 AF XY: 0.492 AC XY: 36552AN XY: 74310
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at