Menu
GeneBe

rs9366816

Variant summary

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

The ENST00000454398.1(HLA-DPA3):n.103-5056A>G 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 0.229 in 151,958 control chromosomes in the GnomAD database, including 4,593 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 0.23 ( 4593 hom., cov: 32)

Consequence

HLA-DPA3
ENST00000454398.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.114
Variant links:
Genes affected
HLA-DPA3 (HGNC:19393): (major histocompatibility complex, class II, DP alpha 3 (pseudogene))

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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105375021XR_926703.3 linkuse as main transcriptn.335-2089A>G intron_variant, non_coding_transcript_variant
LOC105375021XR_001744086.2 linkuse as main transcriptn.335-2089A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HLA-DPA3ENST00000454398.1 linkuse as main transcriptn.103-5056A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.229
AC:
34790
AN:
151840
Hom.:
4581
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.157
Gnomad AMI
AF:
0.115
Gnomad AMR
AF:
0.346
Gnomad ASJ
AF:
0.255
Gnomad EAS
AF:
0.492
Gnomad SAS
AF:
0.186
Gnomad FIN
AF:
0.253
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.225
Gnomad OTH
AF:
0.247
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.229
AC:
34827
AN:
151958
Hom.:
4593
Cov.:
32
AF XY:
0.232
AC XY:
17228
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.157
Gnomad4 AMR
AF:
0.346
Gnomad4 ASJ
AF:
0.255
Gnomad4 EAS
AF:
0.493
Gnomad4 SAS
AF:
0.188
Gnomad4 FIN
AF:
0.253
Gnomad4 NFE
AF:
0.225
Gnomad4 OTH
AF:
0.253
Alfa
AF:
0.228
Hom.:
3839
Bravo
AF:
0.238
Asia WGS
AF:
0.292
AC:
1015
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
11
Dann
Benign
0.30

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: rs9366816; hg19: chr6-33104175; API