17-38853014-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000978.4(RPL23):c.97+8C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000196 in 1,613,392 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_000978.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL23 | NM_000978.4 | c.97+8C>G | splice_region_variant, intron_variant | ENST00000479035.7 | |||
SNORA21 | NR_002576.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL23 | ENST00000479035.7 | c.97+8C>G | splice_region_variant, intron_variant | 1 | NM_000978.4 | P1 | |||
SNORA21 | ENST00000362423.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152122Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000342 AC: 86AN: 251488Hom.: 0 AF XY: 0.000434 AC XY: 59AN XY: 135916
GnomAD4 exome AF: 0.000203 AC: 297AN: 1461152Hom.: 1 Cov.: 30 AF XY: 0.000272 AC XY: 198AN XY: 726926
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at