rs2395360

chr6-33134759-C-Achr6-33134759-C-T

Variant summary

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

The ENST00000454398.1(HLA-DPA3):n.103-3417G>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 0.602 in 152,024 control chromosomes in the GnomAD database, including 28,312 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 0.60 (28312 hom., cov: 31)
• Consequence: HLA-DPA3 ENST00000454398.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375021	XR_926703.3	n.335-450G>T		intron_variant, non_coding_transcript_variant
LOC105375021	XR_001744086.2	n.335-450G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPA3	ENST00000454398.1	n.103-3417G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91405 AN: 151906 Hom.: 28288 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.622

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.602 AC: 91484 AN: 152024 Hom.: 28312 Cov.: 31 AF XY: 0.609 AC XY: 45250 AN XY: 74312

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.625

Alfa AF: 0.591 Hom.: 3231

Bravo AF: 0.599

Asia WGS AF: 0.796 AC: 2766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.1
Dann	Benign	0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2395360; hg19: chr6-33102536;