19-8321642-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001031.5(RPS28):c.40-14C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,555,228 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
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
RPS28
NM_001031.5 splice_polypyrimidine_tract, intron
NM_001031.5 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.43
Genes affected
RPS28 (HGNC:10418): (ribosomal protein S28) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S28E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
Variant 19-8321642-C-T is Benign according to our data. Variant chr19-8321642-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2867901.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
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High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS28 | NM_001031.5 | c.40-14C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000600659.3 | |||
RPS28 | XM_047439201.1 | c.40-14C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS28 | ENST00000600659.3 | c.40-14C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001031.5 | P1 | |||
RPS28 | ENST00000602140.1 | n.76-14C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 | |||||
RPS28 | ENST00000417088.2 | n.9C>T | non_coding_transcript_exon_variant | 1/3 | 2 | ||||
RPS28 | ENST00000449223.3 | n.413-14C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000115 AC: 22AN: 191832Hom.: 0 AF XY: 0.0000576 AC XY: 6AN XY: 104198
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GnomAD4 exome AF: 0.0000214 AC: 30AN: 1402944Hom.: 0 Cov.: 33 AF XY: 0.0000173 AC XY: 12AN XY: 691762
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74454
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 22, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at