8-56069703-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001146227.3(RPS20):c.*35G>A variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00508 in 1,546,176 control chromosomes in the GnomAD database, including 762 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001146227.3 splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS20 | ENST00000519807.5 | c.*35G>A | splice_region_variant | Exon 5 of 6 | 2 | ENSP00000429374.1 | ||||
RPS20 | ENST00000618656.2 | c.*35G>A | splice_region_variant | Exon 4 of 5 | 3 | ENSP00000478703.2 | ||||
RPS20 | ENST00000519807 | c.*35G>A | 3_prime_UTR_variant | Exon 5 of 6 | 2 | ENSP00000429374.1 |
Frequencies
GnomAD3 genomes AF: 0.0101 AC: 1538AN: 152150Hom.: 101 Cov.: 32
GnomAD3 exomes AF: 0.0284 AC: 4369AN: 153994Hom.: 480 AF XY: 0.0214 AC XY: 1747AN XY: 81726
GnomAD4 exome AF: 0.00451 AC: 6291AN: 1393908Hom.: 657 Cov.: 29 AF XY: 0.00380 AC XY: 2614AN XY: 687874
GnomAD4 genome AF: 0.0102 AC: 1559AN: 152268Hom.: 105 Cov.: 32 AF XY: 0.0111 AC XY: 824AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at