chr6-33118170-G-C

Variant names:

• chr6-33118170-G-C
• rs4711314
• ENST00000782909.1:n.59G>C

Variant summary

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

The ENST00000782909.1(ENSG00000291111):​n.59G>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 0.0978 in 152,172 control chromosomes in the GnomAD database, including 787 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 0.098 (787 hom., cov: 32)
• Consequence: ENSG00000291111 ENST00000782909.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.364+950G>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291111	ENST00000782909.1	n.59G>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000301971	ENST00000783126.1	n.795C>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000301971	ENST00000783127.1	n.793C>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0979 AC: 14885 AN: 152054 Hom.: 787 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0731

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0978 AC: 14887 AN: 152172 Hom.: 787 Cov.: 32 AF XY: 0.0958 AC XY: 7129 AN XY: 74402

African (AFR) AF: 0.114 AC: 4732 AN: 41492

American (AMR) AF: 0.132 AC: 2015 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3472

East Asian (EAS) AF: 0.0732 AC: 379 AN: 5176

South Asian (SAS) AF: 0.137 AC: 660 AN: 4806

European-Finnish (FIN) AF: 0.0320 AC: 340 AN: 10618

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0887 AC: 6034 AN: 67994

Other (OTH) AF: 0.121 AC: 255 AN: 2110

Alfa AF: 0.0295 Hom.: 11

Bravo AF: 0.107

Asia WGS AF: 0.100 AC: 348 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	1.6
DANN	Benign	0.67
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs4711314; hg19: chr6-33085947;