rs9268832

Variant names:

• chr6-32460012-T-C
• rs9268832
• ENST00000449413.1:n.152A>G

Variant summary

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

The ENST00000766009.1(ENSG00000299747):​n.335A>G 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 0.61 in 518,956 control chromosomes in the GnomAD database, including 98,045 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 0.60 (27469 hom., cov: 31)
  • Exomes 𝑓: 0.61 (70576 hom.)
• Consequence: ENSG00000299747 ENST00000766009.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43
• Publications: 82 publications found

Genes affected

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

ENSG00000299747 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766009.1. 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.152A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000299747	ENST00000766009.1		n.335A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000299747	ENST00000766007.1		n.-31A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90683 AN: 151852 Hom.: 27452 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.637

GnomAD2 exomes AF: 0.614 AC: 141216 AN: 229982 AF XY: 0.620

Gnomad AFR exome AF: 0.581

Gnomad AMR exome AF: 0.622

Gnomad ASJ exome AF: 0.755

Gnomad EAS exome AF: 0.586

Gnomad FIN exome AF: 0.508

Gnomad NFE exome AF: 0.601

Gnomad OTH exome AF: 0.631

GnomAD4 exome AF: 0.615 AC: 225664 AN: 366986 Hom.: 70576 Cov.: 0 AF XY: 0.623 AC XY: 131049 AN XY: 210406

African (AFR) AF: 0.573 AC: 6027 AN: 10510

American (AMR) AF: 0.625 AC: 22681 AN: 36302

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 8828 AN: 11744

East Asian (EAS) AF: 0.587 AC: 7732 AN: 13172

South Asian (SAS) AF: 0.678 AC: 45263 AN: 66802

European-Finnish (FIN) AF: 0.503 AC: 8618 AN: 17150

Middle Eastern (MID) AF: 0.736 AC: 2098 AN: 2852

European-Non Finnish (NFE) AF: 0.597 AC: 114462 AN: 191842

Other (OTH) AF: 0.599 AC: 9955 AN: 16612

GnomAD4 genome AF: 0.597 AC: 90750 AN: 151970 Hom.: 27469 Cov.: 31 AF XY: 0.596 AC XY: 44298 AN XY: 74276

African (AFR) AF: 0.574 AC: 23780 AN: 41458

American (AMR) AF: 0.664 AC: 10149 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2627 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2908 AN: 5142

South Asian (SAS) AF: 0.649 AC: 3126 AN: 4818

European-Finnish (FIN) AF: 0.504 AC: 5317 AN: 10540

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40588 AN: 67948

Other (OTH) AF: 0.632 AC: 1337 AN: 2114

Alfa AF: 0.599 Hom.: 94599

Bravo AF: 0.611

Asia WGS AF: 0.548 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.25
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs9268832; hg19: chr6-32427789;