rs2797567

Positions:

• chr10-93284178-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000394133.2(RPL17P34):​n.381C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 1,575,004 control chromosomes in the GnomAD database, including 222,031 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.42 (15578 hom., cov: 30)
  • Exomes 𝑓: 0.52 (206453 hom.)
• Consequence: RPL17P34 ENST00000394133.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

RPL17P34 (HGNC:36756): (ribosomal protein L17 pseudogene 34)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL17P34	ENST00000394133.2	n.381C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63659 AN: 151192 Hom.: 15576 Cov.: 30

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.522 AC: 742801 AN: 1423692 Hom.: 206453 Cov.: 36 AF XY: 0.516 AC XY: 366567 AN XY: 709950

Gnomad4 AFR exome AF: 0.184

Gnomad4 AMR exome AF: 0.400

Gnomad4 ASJ exome AF: 0.554

Gnomad4 EAS exome AF: 0.143

Gnomad4 SAS exome AF: 0.283

Gnomad4 FIN exome AF: 0.510

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.495

GnomAD4 genome AF: 0.421 AC: 63674 AN: 151312 Hom.: 15578 Cov.: 30 AF XY: 0.414 AC XY: 30550 AN XY: 73874

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.440

Alfa AF: 0.475 Hom.: 2311

Bravo AF: 0.410

Asia WGS AF: 0.221 AC: 766 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2797567; hg19: chr10-95043935;