rs7766843

Variant names:

• chr6-32462952-C-T
• rs7766843
• ENST00000449413.1:n.77-2865G>A

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-2865G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,000 control chromosomes in the GnomAD database, including 6,390 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 0.29 (6390 hom., cov: 31)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 33 publications found

Genes affected

HLA-DRB9 (HGNC:4957): (major histocompatibility complex, class II, DR beta 9 (pseudogene))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449413.1. 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-DRB9	ENST00000449413.1	TSL:6	n.77-2865G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43502 AN: 151882 Hom.: 6386 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.286 AC: 43535 AN: 152000 Hom.: 6390 Cov.: 31 AF XY: 0.287 AC XY: 21320 AN XY: 74306

African (AFR) AF: 0.343 AC: 14219 AN: 41432

American (AMR) AF: 0.273 AC: 4162 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1261 AN: 5174

South Asian (SAS) AF: 0.237 AC: 1140 AN: 4816

European-Finnish (FIN) AF: 0.354 AC: 3734 AN: 10556

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17420 AN: 67982

Other (OTH) AF: 0.286 AC: 604 AN: 2114

Alfa AF: 0.317 Hom.: 2698

Bravo AF: 0.282

Asia WGS AF: 0.279 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.68
PhyloP100		-0.84

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: rs7766843;

hg19: chr6-32430729;