rs17666267

Variant names:

• chr18-62415985-C-A
• rs17666267
• ENST00000475372.2:n.308C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-62415985-C-A
• chr18-62415985-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000475372.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL17P44	ENST00000475372.2	TSL:6	n.308C>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0639 AC: 820 AN: 12838

American (AMR) AF: 0.206 AC: 7955 AN: 38628

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 2362 AN: 14440

East Asian (EAS) AF: 0.0241 AC: 466 AN: 19306

South Asian (SAS) AF: 0.0625 AC: 4232 AN: 67696

European-Finnish (FIN) AF: 0.210 AC: 5437 AN: 25886

Middle Eastern (MID) AF: 0.132 AC: 203 AN: 1542

European-Non Finnish (NFE) AF: 0.234 AC: 57214 AN: 244060

Other (OTH) AF: 0.186 AC: 4078 AN: 21874

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

African (AFR) AF: 0.0621 AC: 2577 AN: 41518

American (AMR) AF: 0.222 AC: 3390 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3468

East Asian (EAS) AF: 0.0236 AC: 122 AN: 5180

South Asian (SAS) AF: 0.0552 AC: 266 AN: 4816

European-Finnish (FIN) AF: 0.209 AC: 2199 AN: 10542

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15797 AN: 67972

Other (OTH) AF: 0.169 AC: 356 AN: 2112

Alfa AF: 0.102 Hom.: 220

Bravo AF: 0.165

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		3.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17666267;

hg19: chr18-60083218;

COSMIC: COSV72049473;