rs9366816

chr6-33136398-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

Genes affected

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

LOC105375021 (HGNC:):

ACMG classification

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
LOC105375021	XR_926703.3	n.335-2089A>G		intron_variant, non_coding_transcript_variant
LOC105375021	XR_001744086.2	n.335-2089A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPA3	ENST00000454398.1	n.103-5056A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34790 AN: 151840 Hom.: 4581 Cov.: 32

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

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

Other links and lift over

dbSNP: rs9366816; hg19: chr6-33104175;