rs16965654

Variant names:

• chr17-27280666-G-A
• rs16965654
• ENST00000479473.1:n.185G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-27280666-G-A
• chr17-27280666-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000479473.1(RPS16P8):​n.185G>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 0.012 in 202,860 control chromosomes in the GnomAD database, including 57 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 0.015 (55 hom., cov: 32)
  • Exomes 𝑓: 0.0017 (2 hom.)
• Consequence: RPS16P8 ENST00000479473.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94
• Publications: 3 publications found

Genes affected

RPS16P8 (HGNC:35608): (ribosomal protein S16 pseudogene 8)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000479473.1. 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
	RPS16P8	ENST00000479473.1	TSL:6	n.185G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0154 AC: 2351 AN: 152192 Hom.: 55 Cov.: 32

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00504

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00766

GnomAD4 exome AF: 0.00168 AC: 85 AN: 50550 Hom.: 2 Cov.: 0 AF XY: 0.00133 AC XY: 39 AN XY: 29266

African (AFR) AF: 0.0482 AC: 71 AN: 1472

American (AMR) AF: 0.00221 AC: 14 AN: 6338

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 552

East Asian (EAS) AF: 0.00 AC: 0 AN: 3182

South Asian (SAS) AF: 0.00 AC: 0 AN: 5424

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6962

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 74

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 24640

Other (OTH) AF: 0.00 AC: 0 AN: 1906

GnomAD4 genome AF: 0.0155 AC: 2358 AN: 152310 Hom.: 55 Cov.: 32 AF XY: 0.0152 AC XY: 1133 AN XY: 74478

African (AFR) AF: 0.0542 AC: 2252 AN: 41550

American (AMR) AF: 0.00503 AC: 77 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10628

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000162 AC: 11 AN: 68030

Other (OTH) AF: 0.00758 AC: 16 AN: 2110

Alfa AF: 0.00518 Hom.: 8

Bravo AF: 0.0174

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	3.9
DANN	Benign	0.69
PhyloP100		2.9

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: rs16965654;

hg19: chr17-25607692;