rs9902857

chr17-77920078-C-T

Variant summary

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

The 17-77920078-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,058 control chromosomes in the GnomAD database, including 4,838 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 0.24 (4838 hom., cov: 31)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: RNU1-80P ENST00000459500.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

RNU1-80P (HGNC:48422): (RNA, U1 small nuclear 80, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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
RNU1-80P	ENST00000459500.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36286 AN: 151934 Hom.: 4833 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.242

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.239 AC: 36326 AN: 152052 Hom.: 4838 Cov.: 31 AF XY: 0.236 AC XY: 17542 AN XY: 74324

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.0522

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.244

Alfa AF: 0.206 Hom.: 6157

Bravo AF: 0.247

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.028
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9902857; hg19: chr17-75916160;