chr6-32462390-A-C

Variant names:

• chr6-32462390-A-C
• rs9268862
• ENST00000449413.1:n.77-2303T>G

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-2303T>G 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 151,948 control chromosomes in the GnomAD database, including 6,387 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 (6387 hom., cov: 31)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 27 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=-0.88).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DRB9	ENST00000449413.1	TSL:6	n.77-2303T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43495 AN: 151830 Hom.: 6383 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.238

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: 43528 AN: 151948 Hom.: 6387 Cov.: 31 AF XY: 0.287 AC XY: 21318 AN XY: 74274

African (AFR) AF: 0.343 AC: 14197 AN: 41410

American (AMR) AF: 0.273 AC: 4176 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1266 AN: 5176

South Asian (SAS) AF: 0.237 AC: 1139 AN: 4800

European-Finnish (FIN) AF: 0.354 AC: 3744 AN: 10562

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

European-Non Finnish (NFE) AF: 0.256 AC: 17406 AN: 67950

Other (OTH) AF: 0.286 AC: 603 AN: 2108

Alfa AF: 0.273 Hom.: 15135

Bravo AF: 0.282

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.71
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs9268862; hg19: chr6-32430167;