6-33118472-C-T

Variant names:

• chr6-33118472-C-T
• rs3117035
• ENST00000435074.6:n.522C>T

Variant summary

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

The ENST00000684891.2(ENSG00000291111):​n.409C>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 ENST00000684891.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

ENSG00000291111 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.364+1252C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291111	ENST00000435074.6	n.522C>T		non_coding_transcript_exon_variant	Exon 3 of 3	6
ENSG00000291111	ENST00000684891.2	n.409C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000291111	ENST00000686632.1	n.415C>T		non_coding_transcript_exon_variant	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

GnomAD3 exomes AF: 0.421 AC: 2702 AN: 6418 Hom.: 587 AF XY: 0.438 AC XY: 1364 AN XY: 3116

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 SAS exome AF: 0.552

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

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.182

Gnomad4 ASJ exome AF: 0.538

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.519

Gnomad4 FIN exome AF: 0.388

Gnomad4 NFE exome AF: 0.399

Gnomad4 OTH exome AF: 0.453

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

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.356

Alfa AF: 0.417 Hom.: 16430

Bravo AF: 0.329

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117035; hg19: chr6-33086249;