rs1883414

Variant names:

• chr6-33118671-G-A
• rs1883414
• ENST00000435074.7:n.752G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-33118671-G-A
• chr6-33118671-G-C
• chr6-33118671-G-T

Variant summary

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

The ENST00000435074.7(ENSG00000291111):​n.752G>A 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 0.283 in 152,360 control chromosomes in the GnomAD database, including 6,220 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 0.28 (6211 hom., cov: 32)
  • Exomes 𝑓: 0.27 (9 hom.)
• Consequence: ENSG00000291111 ENST00000435074.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 57 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 = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.364+1451G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291111	ENST00000435074.7	n.752G>A		non_coding_transcript_exon_variant	Exon 3 of 3	6
ENSG00000291111	ENST00000684891.3	n.631G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000291111	ENST00000686632.2	n.626G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43011 AN: 151984 Hom.: 6212 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.271 AC: 70 AN: 258 Hom.: 9 Cov.: 0 AF XY: 0.294 AC XY: 53 AN XY: 180

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.254 AC: 62 AN: 244

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.283 AC: 43028 AN: 152102 Hom.: 6211 Cov.: 32 AF XY: 0.283 AC XY: 21067 AN XY: 74370

African (AFR) AF: 0.239 AC: 9901 AN: 41448

American (AMR) AF: 0.265 AC: 4054 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1077 AN: 5180

South Asian (SAS) AF: 0.474 AC: 2282 AN: 4818

European-Finnish (FIN) AF: 0.258 AC: 2729 AN: 10598

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21012 AN: 67988

Other (OTH) AF: 0.291 AC: 612 AN: 2104

Alfa AF: 0.296 Hom.: 21585

Bravo AF: 0.277

Asia WGS AF: 0.316 AC: 1094 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	1.9
DANN	Benign	0.66
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1883414; hg19: chr6-33086448;