ENST00000454398.1:n.103-91T>C

Variant names:

• chr6-33131433-A-G
• rs2294472
• ENST00000782900.1:n.457A>G

Variant summary

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

The ENST00000454398.1(HLA-DPA3):​n.103-91T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,010 control chromosomes in the GnomAD database, including 12,593 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 0.39 (12590 hom., cov: 31)
  • Exomes 𝑓: 0.43 (3 hom.)
• Consequence: HLA-DPA3 ENST00000454398.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 27 publications found

Genes affected

ENSG00000291111 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454398.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375021	NR_190905.1		n.493-91T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291111	ENST00000782900.1		n.457A>G		non_coding_transcript_exon	Exon 3 of 3
	HLA-DPA3	ENST00000454398.1	TSL:6	n.103-91T>C		intron	N/A
	ENSG00000291111	ENST00000782892.1		n.430-9688A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59387 AN: 151862 Hom.: 12574 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 0.429 AC: 12 AN: 28 Hom.: 3 AF XY: 0.571 AC XY: 8 AN XY: 14

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.400 AC: 8 AN: 20

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.391 AC: 59431 AN: 151982 Hom.: 12590 Cov.: 31 AF XY: 0.396 AC XY: 29408 AN XY: 74270

African (AFR) AF: 0.284 AC: 11754 AN: 41440

American (AMR) AF: 0.521 AC: 7955 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3470

East Asian (EAS) AF: 0.762 AC: 3942 AN: 5172

South Asian (SAS) AF: 0.423 AC: 2036 AN: 4812

European-Finnish (FIN) AF: 0.407 AC: 4286 AN: 10536

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26274 AN: 67960

Other (OTH) AF: 0.431 AC: 907 AN: 2106

Alfa AF: 0.402 Hom.: 56178

Bravo AF: 0.400

Asia WGS AF: 0.558 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.54
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2294472; hg19: chr6-33099210;