rs2395360

Variant names:

• chr6-33134759-C-A
• rs2395360
• ENST00000454398.1:n.103-3417G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-33134759-C-A
• chr6-33134759-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454398.1(HLA-DPA3):​n.103-3417G>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

Genes affected

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

ENSG00000291111 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1	n.335-522G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPA3	ENST00000454398.1	n.103-3417G>T		intron_variant	Intron 1 of 1	6
ENSG00000291111	ENST00000782892.1	n.430-6362C>A		intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782893.1	n.404-6362C>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.488 AC: 20235 AN: 41448

American (AMR) AF: 0.669 AC: 10228 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2509 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4800 AN: 5174

South Asian (SAS) AF: 0.767 AC: 3702 AN: 4824

European-Finnish (FIN) AF: 0.633 AC: 6671 AN: 10538

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41324 AN: 67978

Other (OTH) AF: 0.625 AC: 1316 AN: 2104

Alfa AF: 0.587 Hom.: 3324

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
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2395360; hg19: chr6-33102536;