6-32459971-C-T

Variant names:

• chr6-32459971-C-T
• rs9268831
• ENST00000449413.1:n.193G>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.193G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.523 in 519,710 control chromosomes in the GnomAD database, including 72,800 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 0.51 (20255 hom., cov: 32)
  • Exomes 𝑓: 0.53 (52545 hom.)
• Consequence: HLA-DRB9 ENST00000449413.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.97
• Publications: 54 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=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.599 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.193G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000299747	ENST00000766007.1		n.11G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000299747	ENST00000766008.1		n.14G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77774 AN: 151910 Hom.: 20232 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.535

GnomAD2 exomes AF: 0.541 AC: 124860 AN: 230910 AF XY: 0.538

Gnomad AFR exome AF: 0.519

Gnomad AMR exome AF: 0.672

Gnomad ASJ exome AF: 0.634

Gnomad EAS exome AF: 0.579

Gnomad FIN exome AF: 0.429

Gnomad NFE exome AF: 0.498

Gnomad OTH exome AF: 0.539

GnomAD4 exome AF: 0.527 AC: 193725 AN: 367682 Hom.: 52545 Cov.: 0 AF XY: 0.527 AC XY: 111143 AN XY: 210772

African (AFR) AF: 0.512 AC: 5386 AN: 10510

American (AMR) AF: 0.672 AC: 24396 AN: 36300

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 7456 AN: 11744

East Asian (EAS) AF: 0.562 AC: 7408 AN: 13170

South Asian (SAS) AF: 0.549 AC: 36860 AN: 67178

European-Finnish (FIN) AF: 0.427 AC: 7455 AN: 17472

Middle Eastern (MID) AF: 0.646 AC: 1841 AN: 2852

European-Non Finnish (NFE) AF: 0.493 AC: 94491 AN: 191842

Other (OTH) AF: 0.508 AC: 8432 AN: 16614

GnomAD4 genome AF: 0.512 AC: 77846 AN: 152028 Hom.: 20255 Cov.: 32 AF XY: 0.512 AC XY: 38069 AN XY: 74318

African (AFR) AF: 0.514 AC: 21336 AN: 41476

American (AMR) AF: 0.610 AC: 9317 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2189 AN: 3472

East Asian (EAS) AF: 0.556 AC: 2866 AN: 5154

South Asian (SAS) AF: 0.506 AC: 2435 AN: 4816

European-Finnish (FIN) AF: 0.432 AC: 4559 AN: 10552

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33459 AN: 67956

Other (OTH) AF: 0.534 AC: 1127 AN: 2112

Alfa AF: 0.507 Hom.: 75909

Bravo AF: 0.528

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.72
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs9268831; hg19: chr6-32427748;