Variant 6-33131189-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The XR_926703.3(LOC105375021):n.565-90G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,098 control chromosomes in the GnomAD database, including 17,024 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 0.46 ( 17009 hom., cov: 32)

Exomes 𝑓: 0.42 ( 15 hom. )

Consequence

LOC105375021
XR_926703.3 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.430

Variant links:

Genes affected

LOC105375021 (HGNC:):

LOC105375021 links:

HLA-DPA3 (HGNC:19393): (major histocompatibility complex, class II, DP alpha 3 (pseudogene))

HLA-DPA3 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375021	XR_926703.3 linkuse as main transcript	n.565-90G>T		intron_variant, non_coding_transcript_variant
LOC105375021	XR_001744086.2 linkuse as main transcript	n.710+8G>T		splice_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPA3	ENST00000454398.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69359

AN:

151836

Hom.:

16996

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.491

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.642

Gnomad EAS

AF:

0.771

Gnomad SAS

AF:

0.588

Gnomad FIN

AF:

0.480

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.493

GnomAD4 exome

AF:

0.424

AC:

AN:

144

Hom.:

Cov.:

AF XY:

0.429

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.625

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.667

Gnomad4 NFE exome

AF:

0.440

Gnomad4 OTH exome

AF:

0.143

GnomAD4 genome

AF:

0.457

AC:

69403

AN:

151954

Hom.:

17009

Cov.:

AF XY:

0.463

AC XY:

34407

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.296

Gnomad4 AMR

AF:

0.572

Gnomad4 ASJ

AF:

0.642

Gnomad4 EAS

AF:

0.772

Gnomad4 SAS

AF:

0.590

Gnomad4 FIN

AF:

0.480

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.497

Alfa

AF:

0.492

Hom.:

31241

Bravo

AF:

0.459

Asia WGS

AF:

0.616

AC:

2142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.4

DANN

Benign

0.77

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