rs62030476

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000363564.1(RNA5-8SP2):​n.*12G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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 0.50 ( 5 hom., cov: 84)
Exomes 𝑓: 0.36 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RNA5-8SP2
ENST00000363564.1 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.430
Variant links:
Genes affected
RNA5-8SP2 (HGNC:41956): (RNA, 5.8S ribosomal pseudogene 2)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BA1
GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.425 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
RNA5-8SP2ENST00000363564.1 linkn.*12G>A downstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
76158
AN:
152306
Hom.:
5
Cov.:
84
FAILED QC
Gnomad AFR
AF:
0.500
Gnomad AMI
AF:
0.500
Gnomad AMR
AF:
0.500
Gnomad ASJ
AF:
0.500
Gnomad EAS
AF:
0.500
Gnomad SAS
AF:
0.500
Gnomad FIN
AF:
0.500
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.500
Gnomad OTH
AF:
0.500
GnomAD4 exome
AF:
0.359
AC:
71007
AN:
197658
Hom.:
0
Cov.:
0
AF XY:
0.351
AC XY:
39450
AN XY:
112522
show subpopulations
Gnomad4 AFR exome
AF:
0.318
Gnomad4 AMR exome
AF:
0.327
Gnomad4 ASJ exome
AF:
0.236
Gnomad4 EAS exome
AF:
0.324
Gnomad4 SAS exome
AF:
0.347
Gnomad4 FIN exome
AF:
0.397
Gnomad4 NFE exome
AF:
0.369
Gnomad4 OTH exome
AF:
0.378
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.500
AC:
76217
AN:
152424
Hom.:
5
Cov.:
84
AF XY:
0.500
AC XY:
37274
AN XY:
74544
show subpopulations
Gnomad4 AFR
AF:
0.500
Gnomad4 AMR
AF:
0.500
Gnomad4 ASJ
AF:
0.500
Gnomad4 EAS
AF:
0.500
Gnomad4 SAS
AF:
0.500
Gnomad4 FIN
AF:
0.500
Gnomad4 NFE
AF:
0.500
Gnomad4 OTH
AF:
0.500
Alfa
AF:
0.383
Hom.:
3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
CADD
Benign
9.1
DANN
Benign
0.88

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs62030476; hg19: chr16-33965589; COSMIC: COSV63177590; API