6-33118472-C-T

Variant names:

• chr6-33118472-C-T
• rs3117035
• ENST00000435074.7:n.553C>T

Variant summary

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

The ENST00000684891.3(ENSG00000291111):​n.432C>T 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 0.354 in 155,312 control chromosomes in the GnomAD database, including 10,705 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 0.35 (10249 hom., cov: 31)
  • Exomes 𝑓: 0.46 (456 hom.)
• Consequence: ENSG00000291111 ENST00000684891.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 31 publications found

Genes affected

ENSG00000291111 (HGNC:):

HLA-DPB2 (HGNC:4941): (major histocompatibility complex, class II, DP beta 2 (pseudogene))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000684891.3. 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
	HLA-DPB2	NR_001435.2		n.364+1252C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291111	ENST00000435074.7	TSL:6	n.553C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000291111	ENST00000684891.3		n.432C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000291111	ENST00000686632.2		n.427C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53151 AN: 151178 Hom.: 10250 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.359

GnomAD2 exomes AF: 0.421 AC: 2702 AN: 6418 AF XY: 0.438

Gnomad AFR exome AF: 0.158

Gnomad AMR exome AF: 0.254

Gnomad ASJ exome AF: 0.599

Gnomad EAS exome AF: 0.287

Gnomad FIN exome AF: 0.333

Gnomad NFE exome AF: 0.435

Gnomad OTH exome AF: 0.420

GnomAD4 exome AF: 0.459 AC: 1844 AN: 4014 Hom.: 456 Cov.: 0 AF XY: 0.453 AC XY: 1090 AN XY: 2404

African (AFR) AF: 0.163 AC: 16 AN: 98

American (AMR) AF: 0.182 AC: 4 AN: 22

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 14 AN: 26

East Asian (EAS) AF: 0.333 AC: 18 AN: 54

South Asian (SAS) AF: 0.519 AC: 196 AN: 378

European-Finnish (FIN) AF: 0.388 AC: 186 AN: 480

Middle Eastern (MID) AF: 0.531 AC: 868 AN: 1636

European-Non Finnish (NFE) AF: 0.399 AC: 416 AN: 1042

Other (OTH) AF: 0.453 AC: 126 AN: 278

GnomAD4 genome AF: 0.351 AC: 53162 AN: 151298 Hom.: 10249 Cov.: 31 AF XY: 0.354 AC XY: 26165 AN XY: 73928

African (AFR) AF: 0.201 AC: 8257 AN: 41122

American (AMR) AF: 0.290 AC: 4409 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1976 AN: 3460

East Asian (EAS) AF: 0.378 AC: 1931 AN: 5112

South Asian (SAS) AF: 0.551 AC: 2644 AN: 4798

European-Finnish (FIN) AF: 0.407 AC: 4272 AN: 10500

Middle Eastern (MID) AF: 0.490 AC: 142 AN: 290

European-Non Finnish (NFE) AF: 0.419 AC: 28390 AN: 67800

Other (OTH) AF: 0.356 AC: 750 AN: 2106

Alfa AF: 0.398 Hom.: 24486

Bravo AF: 0.329

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3117035; hg19: chr6-33086249;