chr15-82536888-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001021.6(RPS17):c.328-7G>A 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 0.00232 in 1,613,936 control chromosomes in the GnomAD database, including 6 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 Likely benign (★★).
Frequency
Consequence
NM_001021.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS17 | NM_001021.6 | c.328-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000647841.1 | |||
RPS17 | NR_111943.2 | n.650-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
RPS17 | NR_111944.3 | n.478-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS17 | ENST00000647841.1 | c.328-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001021.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00205 AC: 312AN: 152162Hom.: 2 Cov.: 32
GnomAD4 exome AF: 0.00235 AC: 3428AN: 1461656Hom.: 4 Cov.: 31 AF XY: 0.00237 AC XY: 1720AN XY: 727138
GnomAD4 genome AF: 0.00205 AC: 312AN: 152280Hom.: 2 Cov.: 32 AF XY: 0.00212 AC XY: 158AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 16, 2021 | - - |
Diamond-Blackfan anemia 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at