Variant rs62030476 details in Genebe, Genetics Data Aggregator

Variant summary

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

The 16-34163122-G-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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.430

Variant links:

Genes affected

RNA5-8SP2 (HGNC:41956): (RNA, 5.8S ribosomal pseudogene 2)

RNA5-8SP2 links:

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNA5-8SP2	ENST00000363564.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

76158

AN:

152306

Hom.:

Cov.:

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.:

Cov.:

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.:

Cov.:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over