chr19-23827935-T-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001355283.3(RPSA2):c.774T>A(p.Pro258=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 890,106 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 25)
Exomes 𝑓: 0.0016 ( 2 hom. )
Consequence
RPSA2
NM_001355283.3 synonymous
NM_001355283.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.269
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 19-23827935-T-A is Benign according to our data. Variant chr19-23827935-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2649666.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.269 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPSA2 | NM_001355283.3 | c.774T>A | p.Pro258= | synonymous_variant | 4/4 | ENST00000484897.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPSA2 | ENST00000484897.4 | c.774T>A | p.Pro258= | synonymous_variant | 4/4 | NM_001355283.3 | P1 | ||
ENST00000472297.2 | n.214-3662T>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000599944.1 | n.151-753A>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00134 AC: 203AN: 151302Hom.: 0 Cov.: 25
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GnomAD3 exomes AF: 0.000985 AC: 63AN: 63966Hom.: 0 AF XY: 0.00105 AC XY: 34AN XY: 32396
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GnomAD4 exome AF: 0.00163 AC: 1204AN: 738686Hom.: 2 Cov.: 10 AF XY: 0.00162 AC XY: 631AN XY: 388926
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GnomAD4 genome ? AF: 0.00134 AC: 203AN: 151420Hom.: 0 Cov.: 25 AF XY: 0.00131 AC XY: 97AN XY: 73970
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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 | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | RPSAP58: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at