6-32460012-T-C

Position:

• chr6-32460012-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449413.1(HLA-DRB9):​n.152A>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: HLA-DRB9 ENST00000449413.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43

Genes affected

HLA-DRB9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DRB9		n.32460012T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.152A>G		non_coding_transcript_exon_variant	2/2	6

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

GnomAD3 exomes AF: 0.614 AC: 141216 AN: 229982 Hom.: 44104 AF XY: 0.620 AC XY: 78748 AN XY: 127056

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 SAS exome AF: 0.675

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

Gnomad4 AFR exome AF: 0.573

Gnomad4 AMR exome AF: 0.625

Gnomad4 ASJ exome AF: 0.752

Gnomad4 EAS exome AF: 0.587

Gnomad4 SAS exome AF: 0.678

Gnomad4 FIN exome AF: 0.503

Gnomad4 NFE exome AF: 0.597

Gnomad4 OTH exome AF: 0.599

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

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.632

Alfa AF: 0.611 Hom.: 37308

Bravo AF: 0.611

Asia WGS AF: 0.548 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268832; hg19: chr6-32427789;