19-23827863-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001355283.3(RPSA2):c.702C>T(p.Pro234=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000751 in 1,151,346 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 0.00092 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00073 (0 hom.)
• Consequence: RPSA2 NM_001355283.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.480

Genes affected

RPSA2 (HGNC:36809): (ribosomal protein SA 2)

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 19-23827863-C-T is Benign according to our data. Variant chr19-23827863-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649665.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.48 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPSA2	NM_001355283.3	c.702C>T	p.Pro234=	synonymous_variant	4/4	ENST00000484897.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPSA2	ENST00000484897.4	c.702C>T	p.Pro234=	synonymous_variant	4/4		NM_001355283.3	P1
	ENST00000472297.2	n.214-3734C>T		intron_variant, non_coding_transcript_variant
	ENST00000599944.1	n.151-681G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.000922 AC: 140 AN: 151766 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000315

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000329

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.000418

Gnomad FIN AF: 0.000284

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00154

Gnomad OTH AF: 0.000481

GnomAD3 exomes AF: 0.00113 AC: 73 AN: 64652 Hom.: 0 AF XY: 0.00114 AC XY: 37 AN XY: 32420

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000540

Gnomad ASJ exome AF: 0.00298

Gnomad EAS exome AF: 0.000873

Gnomad SAS exome AF: 0.000628

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00170

Gnomad OTH exome AF: 0.00190

GnomAD4 exome AF: 0.000725 AC: 725 AN: 999462 Hom.: 0 Cov.: 13 AF XY: 0.000720 AC XY: 369 AN XY: 512570

Gnomad4 AFR exome AF: 0.000350

Gnomad4 AMR exome AF: 0.000600

Gnomad4 ASJ exome AF: 0.00201

Gnomad4 EAS exome AF: 0.000418

Gnomad4 SAS exome AF: 0.000406

Gnomad4 FIN exome AF: 0.000334

Gnomad4 NFE exome AF: 0.000769

Gnomad4 OTH exome AF: 0.000616

GnomAD4 genome AF: 0.000922 AC: 140 AN: 151884 Hom.: 0 Cov.: 31 AF XY: 0.000835 AC XY: 62 AN XY: 74214

Gnomad4 AFR AF: 0.000314

Gnomad4 AMR AF: 0.000328

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.000776

Gnomad4 SAS AF: 0.000419

Gnomad4 FIN AF: 0.000284

Gnomad4 NFE AF: 0.00155

Gnomad4 OTH AF: 0.000476

Alfa AF: 0.00139 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

RPSAP58: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.8
Dann	Benign	0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs201171553; hg19: chr19-24010665;