Variant rs1638152 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_023383.1(DTX2P1-UPK3BP1-PMS2P11):n.541G>A variant causes a splice region, non coding transcript exon 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 0.36 ( 6 hom., cov: 32)

Exomes 𝑓: 0.37 ( 53 hom. )

Failed GnomAD Quality Control

Consequence

DTX2P1-UPK3BP1-PMS2P11
NR_023383.1 splice_region, non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.71

Variant links:

Genes affected

DTX2P1 (HGNC:42352): (DTX2 pseudogene 1)

DTX2P1 links:

DTX2P1-UPK3BP1-PMS2P11 (HGNC:):

DTX2P1-UPK3BP1-PMS2P11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DTX2P1-UPK3BP1-PMS2P11	NR_023383.1 linkuse as main transcript	n.541G>A		splice_region_variant, non_coding_transcript_exon_variant	3/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DTX2P1	ENST00000425797.2 linkuse as main transcript	n.1143G>A		splice_region_variant, non_coding_transcript_exon_variant	5/8

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

44304

AN:

121904

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.352

Gnomad AMI

AF:

0.381

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.256

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.388

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.375

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.371

AC:

318482

AN:

858638

Hom.:

Cov.:

AF XY:

0.374

AC XY:

166391

AN XY:

444616

show subpopulations

Gnomad4 AFR exome

AF:

0.315

Gnomad4 AMR exome

AF:

0.380

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.258

Gnomad4 SAS exome

AF:

0.411

Gnomad4 FIN exome

AF:

0.304

Gnomad4 NFE exome

AF:

0.377

Gnomad4 OTH exome

AF:

0.365

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.364

AC:

44357

AN:

122014

Hom.:

Cov.:

AF XY:

0.358

AC XY:

21425

AN XY:

59832

show subpopulations

Gnomad4 AFR

AF:

0.352

Gnomad4 AMR

AF:

0.353

Gnomad4 ASJ

AF:

0.420

Gnomad4 EAS

AF:

0.256

Gnomad4 SAS

AF:

0.388

Gnomad4 FIN

AF:

0.284

Gnomad4 NFE

AF:

0.387

Gnomad4 OTH

AF:

0.377

Alfa

AF:

0.234

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.93

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