Variant rs850084 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NR_158194.1(DPY19L2P3):n.1175A>C 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 0.265 in 1,555,664 control chromosomes in the GnomAD database, including 56,589 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 0.28 ( 6078 hom., cov: 29)

Exomes 𝑓: 0.26 ( 50511 hom. )

Consequence

DPY19L2P3
NR_158194.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.700

Variant links:

Genes affected

DPY19L2P3 (HGNC:22367): (DPY19L2 pseudogene 3)

DPY19L2P3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L2P3	NR_158194.1 linkuse as main transcript	n.1175A>C		non_coding_transcript_exon_variant	7/9

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
DPY19L2P3	ENST00000414296.2 linkuse as main transcript	n.1687A>C	non_coding_transcript_exon_variant	17/19
DPY19L2P3	ENST00000688393.1 linkuse as main transcript	n.792A>C	non_coding_transcript_exon_variant	11/12
DPY19L2P3	ENST00000689485.1 linkuse as main transcript	n.261A>C	non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

41803

AN:

150908

Hom.:

6082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.328

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.283

GnomAD4 exome

AF:

0.263

AC:

369682

AN:

1404640

Hom.:

50511

Cov.:

AF XY:

0.264

AC XY:

183967

AN XY:

697310

show subpopulations

Gnomad4 AFR exome

AF:

0.236

Gnomad4 AMR exome

AF:

0.416

Gnomad4 ASJ exome

AF:

0.202

Gnomad4 EAS exome

AF:

0.333

Gnomad4 SAS exome

AF:

0.314

Gnomad4 FIN exome

AF:

0.305

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.265

GnomAD4 genome

AF:

0.277

AC:

41821

AN:

151024

Hom.:

6078

Cov.:

AF XY:

0.284

AC XY:

20899

AN XY:

73694

show subpopulations

Gnomad4 AFR

AF:

0.249

Gnomad4 AMR

AF:

0.394

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.315

Gnomad4 SAS

AF:

0.347

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.259

Gnomad4 OTH

AF:

0.290

Alfa

AF:

0.267

Hom.:

5772

Bravo

AF:

0.282

Asia WGS

AF:

0.351

AC:

1218

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

7.2

DANN

Benign

0.76

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