16-18784831-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001019.5(RPS15A):c.214-8T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 1,587,584 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_001019.5 splice_region, splice_polypyrimidine_tract, 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 |
---|---|---|---|---|---|---|---|
RPS15A | NM_001019.5 | c.214-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000322989.8 | |||
RPS15A | NM_001030009.2 | c.214-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS15A | ENST00000322989.8 | c.214-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001019.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000859 AC: 2AN: 232960Hom.: 0 AF XY: 0.00000793 AC XY: 1AN XY: 126106
GnomAD4 exome AF: 0.0000230 AC: 33AN: 1435398Hom.: 0 Cov.: 26 AF XY: 0.0000238 AC XY: 17AN XY: 714500
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74344
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at