chr6-33092651-C-T

Position:

• chr6-33092651-C-T

Variant summary

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

The ENST00000433582.1(HLA-DPA2):​n.300+242G>A 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 0.0538 in 152,238 control chromosomes in the GnomAD database, including 336 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 0.054 (336 hom., cov: 32)
• Consequence: HLA-DPA2 ENST00000433582.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

Genes affected

HLA-DPA2 (HGNC:4939): (major histocompatibility complex, class II, DP alpha 2 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.300+242G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8199 AN: 152120 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0945

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0460

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0368

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0538 AC: 8198 AN: 152238 Hom.: 336 Cov.: 32 AF XY: 0.0520 AC XY: 3867 AN XY: 74428

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.0742

Gnomad4 SAS AF: 0.0802

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.0368

Gnomad4 OTH AF: 0.0693

Alfa AF: 0.0408 Hom.: 93

Bravo AF: 0.0588

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7763822; hg19: chr6-33060428;