rs705704

chr12-56041628-G-Achr12-56041628-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000356464.10(RPS26):c.-356-183G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 173,556 control chromosomes in the GnomAD database, including 6,851 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.26 (5525 hom., cov: 29)
  • Exomes 𝑓: 0.31 (1326 hom.)
• Consequence: RPS26 ENST00000356464.10 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0430

Genes affected

RPS26 (HGNC:10414): (ribosomal protein S26) This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S26E family of ribosomal proteins. Mutations in this gene are found in Diamond-Blackfan anemia 10. There are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Aug 2017]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 12-56041628-G-A is Benign according to our data. Variant chr12-56041628-G-A is described in ClinVar as [Benign]. Clinvar id is 1259753.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS26	ENST00000356464.10	c.-356-183G>A		intron_variant		1		P1
	ENST00000551846.1	n.179C>T		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes AF: 0.260 AC: 38752 AN: 149122 Hom.: 5524 Cov.: 29

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.310 AC: 7544 AN: 24328 Hom.: 1326 Cov.: 0 AF XY: 0.310 AC XY: 3988 AN XY: 12868

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.219

Gnomad4 ASJ exome AF: 0.377

Gnomad4 EAS exome AF: 0.230

Gnomad4 SAS exome AF: 0.270

Gnomad4 FIN exome AF: 0.354

Gnomad4 NFE exome AF: 0.362

Gnomad4 OTH exome AF: 0.334

GnomAD4 genome AF: 0.260 AC: 38749 AN: 149228 Hom.: 5525 Cov.: 29 AF XY: 0.256 AC XY: 18675 AN XY: 72810

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.273

Alfa AF: 0.308 Hom.: 7453

Bravo AF: 0.247

Asia WGS AF: 0.180 AC: 629 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	5.3
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs705704; hg19: chr12-56435412;