rs3829795

Variant names:

• chr1-179576534-G-A
• rs3829795
• ENST00000516066.1:n.*185G>A

Variant summary

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

The ENST00000516066.1(RNU5F-2P):​n.*185G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,982 control chromosomes in the GnomAD database, including 8,008 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 0.31 (8008 hom., cov: 32)
• Consequence: RNU5F-2P ENST00000516066.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 9 publications found

Genes affected

RNU5F-2P (HGNC:42510): (RNA, U5F small nuclear 2, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNU5F-2P	ENST00000516066.1	n.*185G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47635 AN: 151864 Hom.: 8015 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.318

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.313 AC: 47643 AN: 151982 Hom.: 8008 Cov.: 32 AF XY: 0.316 AC XY: 23450 AN XY: 74278

African (AFR) AF: 0.201 AC: 8325 AN: 41454

American (AMR) AF: 0.315 AC: 4804 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2584 AN: 5162

South Asian (SAS) AF: 0.343 AC: 1651 AN: 4816

European-Finnish (FIN) AF: 0.372 AC: 3920 AN: 10526

Middle Eastern (MID) AF: 0.303 AC: 88 AN: 290

European-Non Finnish (NFE) AF: 0.355 AC: 24098 AN: 67972

Other (OTH) AF: 0.318 AC: 671 AN: 2110

Alfa AF: 0.336 Hom.: 10824

Bravo AF: 0.304

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.55
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3829795; hg19: chr1-179545669;