rs6573295

Positions:

• chr14-60212535-T-C

Variant summary

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

The ENST00000491913.2(RPL17P2):​n.378A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0604 in 491,080 control chromosomes in the GnomAD database, including 1,532 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 0.077 (747 hom., cov: 32)
  • Exomes 𝑓: 0.053 (785 hom.)
• Consequence: RPL17P2 ENST00000491913.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.36

Genes affected

RPL17P2 (HGNC:23540): (ribosomal protein L17 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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
RPL17P2	ENST00000491913.2	n.378A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0765 AC: 11634 AN: 152156 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0660

GnomAD4 exome AF: 0.0531 AC: 17989 AN: 338806 Hom.: 785 Cov.: 0 AF XY: 0.0551 AC XY: 10757 AN XY: 195272

Gnomad4 AFR exome AF: 0.159

Gnomad4 AMR exome AF: 0.0470

Gnomad4 ASJ exome AF: 0.0826

Gnomad4 EAS exome AF: 0.161

Gnomad4 SAS exome AF: 0.0830

Gnomad4 FIN exome AF: 0.0176

Gnomad4 NFE exome AF: 0.0314

Gnomad4 OTH exome AF: 0.0534

GnomAD4 genome AF: 0.0767 AC: 11681 AN: 152274 Hom.: 747 Cov.: 32 AF XY: 0.0760 AC XY: 5656 AN XY: 74460

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0544

Gnomad4 ASJ AF: 0.0904

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0872

Gnomad4 FIN AF: 0.0160

Gnomad4 NFE AF: 0.0328

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0585 Hom.: 73

Bravo AF: 0.0828

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6573295; hg19: chr14-60679253;