4-39454848-T-C
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000661.5(RPL9):c.472+16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,610,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000661.5 intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -10 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000661.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RPL9 | NM_000661.5 | MANE Select | c.472+16A>G | intron | N/A | NP_000652.2 | |||
| RPL9 | NM_001024921.4 | c.472+16A>G | intron | N/A | NP_001020092.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RPL9 | ENST00000295955.14 | TSL:1 MANE Select | c.472+16A>G | intron | N/A | ENSP00000346022.7 | |||
| RPL9 | ENST00000449470.6 | TSL:1 | c.472+16A>G | intron | N/A | ENSP00000400467.2 | |||
| RPL9 | ENST00000503277.6 | TSL:2 | c.556+16A>G | intron | N/A | ENSP00000494836.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000160 AC: 4AN: 250622 AF XY: 0.00000738 show subpopulations
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1458382Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 725664 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74382 show subpopulations
Age Distribution
ClinVar
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at