19-23827935-T-A

Variant names:

• chr19-23827935-T-A
• rs549448615
• NM_001355283.3:c.774T>A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001355283.3(RPSA2):​c.774T>A​(p.Pro258Pro) 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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.269

Genes affected

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

ENSG00000233836 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -11 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.
• BS2: High Homozygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPSA2	NM_001355283.3	c.774T>A	p.Pro258Pro	synonymous_variant	Exon 4 of 4	ENST00000484897.4	NP_001342212.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPSA2	ENST00000484897.4	c.774T>A	p.Pro258Pro	synonymous_variant	Exon 4 of 4	6	NM_001355283.3	ENSP00000509526.1

Frequencies

GnomAD3 genomes AF: 0.00134 AC: 203 AN: 151302 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000462

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00143

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.000971

GnomAD3 exomes AF: 0.000985 AC: 63 AN: 63966 Hom.: 0 AF XY: 0.00105 AC XY: 34 AN XY: 32396

Gnomad AFR exome AF: 0.000165

Gnomad AMR exome AF: 0.000978

Gnomad ASJ exome AF: 0.00113

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00215

Gnomad NFE exome AF: 0.00163

Gnomad OTH exome AF: 0.000961

GnomAD4 exome AF: 0.00163 AC: 1204 AN: 738686 Hom.: 2 Cov.: 10 AF XY: 0.00162 AC XY: 631 AN XY: 388926

Gnomad4 AFR exome AF: 0.0000975

Gnomad4 AMR exome AF: 0.000590

Gnomad4 ASJ exome AF: 0.00266

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00280

Gnomad4 NFE exome AF: 0.00204

Gnomad4 OTH exome AF: 0.00103

GnomAD4 genome AF: 0.00134 AC: 203 AN: 151420 Hom.: 0 Cov.: 25 AF XY: 0.00131 AC XY: 97 AN XY: 73970

Gnomad4 AFR AF: 0.000243

Gnomad4 AMR AF: 0.000461

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00143

Gnomad4 NFE AF: 0.00237

Gnomad4 OTH AF: 0.000961

Alfa AF: 0.00366 Hom.: 0

Bravo AF: 0.000975

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

RPSA2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	5.3
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs549448615; hg19: chr19-24010737;