chr6-33093063-C-G

Variant names:

• chr6-33093063-C-G
• rs7764491
• ENST00000433582.1:n.130G>C

Variant summary

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

The ENST00000433582.1(HLA-DPA2):​n.130G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0538 in 152,490 control chromosomes in the GnomAD database, including 330 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 (330 hom., cov: 32)
  • Exomes 𝑓: 0.019 (0 hom.)
• Consequence: HLA-DPA2 ENST00000433582.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 15 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433582.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPA2	ENST00000433582.1	TSL:6	n.130G>C		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8198 AN: 152216 Hom.: 330 Cov.: 32

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0735

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.00320

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0368

Gnomad OTH AF: 0.0702

GnomAD4 exome AF: 0.0192 AC: 3 AN: 156 Hom.: 0 Cov.: 0 AF XY: 0.0222 AC XY: 2 AN XY: 90

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0221 AC: 3 AN: 136

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.0538 AC: 8197 AN: 152334 Hom.: 330 Cov.: 32 AF XY: 0.0518 AC XY: 3861 AN XY: 74496

African (AFR) AF: 0.0944 AC: 3923 AN: 41564

American (AMR) AF: 0.0457 AC: 700 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3466

East Asian (EAS) AF: 0.0735 AC: 381 AN: 5182

South Asian (SAS) AF: 0.0800 AC: 386 AN: 4828

European-Finnish (FIN) AF: 0.00320 AC: 34 AN: 10622

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0368 AC: 2502 AN: 68038

Other (OTH) AF: 0.0690 AC: 146 AN: 2116

Alfa AF: 0.0421 Hom.: 23

Bravo AF: 0.0588

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	5.6
DANN	Benign	0.41
PhyloP100		0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7764491;

hg19: chr6-33060840;