rs17666267

chr18-62415985-C-Achr18-62415985-C-T

Variant summary

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

The ENST00000475372.2(RPL17P44):n.308C>A 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 0.181 in 598,344 control chromosomes in the GnomAD database, including 11,652 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 0.17 (2677 hom., cov: 32)
  • Exomes 𝑓: 0.19 (8975 hom.)
• Consequence: RPL17P44 ENST00000475372.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.04

Genes affected

RPL17P44 (HGNC:36396): (ribosomal protein L17 pseudogene 44)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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
RPL17P44	ENST00000475372.2	n.308C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25419 AN: 151956 Hom.: 2678 Cov.: 32

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0548

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.185 AC: 82767 AN: 446270 Hom.: 8975 Cov.: 0 AF XY: 0.177 AC XY: 44252 AN XY: 250040

Gnomad4 AFR exome AF: 0.0639

Gnomad4 AMR exome AF: 0.206

Gnomad4 ASJ exome AF: 0.164

Gnomad4 EAS exome AF: 0.0241

Gnomad4 SAS exome AF: 0.0625

Gnomad4 FIN exome AF: 0.210

Gnomad4 NFE exome AF: 0.234

Gnomad4 OTH exome AF: 0.186

GnomAD4 genome AF: 0.167 AC: 25415 AN: 152074 Hom.: 2677 Cov.: 32 AF XY: 0.165 AC XY: 12247 AN XY: 74322

Gnomad4 AFR AF: 0.0621

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0236

Gnomad4 SAS AF: 0.0552

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.169

Alfa AF: 0.102 Hom.: 216

Bravo AF: 0.165

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	1.0
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17666267; hg19: chr18-60083218; COSMIC: COSV72049473;