6-32460995-A-G

Variant names:

• chr6-32460995-A-G
• rs9268839
• ENST00000449413.1:n.77-908T>C

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-908T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,052 control chromosomes in the GnomAD database, including 11,641 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 0.38 (11641 hom., cov: 32)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 56 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DRB9	ENST00000449413.1	TSL:6	n.77-908T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57892 AN: 151934 Hom.: 11636 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.381 AC: 57924 AN: 152052 Hom.: 11641 Cov.: 32 AF XY: 0.381 AC XY: 28300 AN XY: 74302

African (AFR) AF: 0.270 AC: 11193 AN: 41480

American (AMR) AF: 0.432 AC: 6604 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1958 AN: 5170

South Asian (SAS) AF: 0.342 AC: 1646 AN: 4818

European-Finnish (FIN) AF: 0.444 AC: 4674 AN: 10532

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28705 AN: 67980

Other (OTH) AF: 0.385 AC: 814 AN: 2114

Alfa AF: 0.400 Hom.: 25507

Bravo AF: 0.384

Asia WGS AF: 0.326 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.51
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9268839; hg19: chr6-32428772;