chr6-32473323-A-C

Variant names:

• chr6-32473323-A-C
• rs9269081
• ENST00000846999.1:n.303T>G

Variant summary

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

The ENST00000846999.1(ENSG00000310084):​n.303T>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 0.701 in 739,836 control chromosomes in the GnomAD database, including 184,426 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 0.69 (36052 hom., cov: 31)
  • Exomes 𝑓: 0.70 (148374 hom.)
• Consequence: ENSG00000310084 ENST00000846999.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.96
• Publications: 27 publications found

Genes affected

ENSG00000310084 (HGNC:):

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 = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310084	ENST00000846999.1	n.303T>G		non_coding_transcript_exon_variant	Exon 1 of 1
HLA-DRB9	ENST00000449413.1	n.76+102T>G		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104046 AN: 151818 Hom.: 36018 Cov.: 31

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.698

GnomAD4 exome AF: 0.705 AC: 414365 AN: 587900 Hom.: 148374 AF XY: 0.692 AC XY: 221018 AN XY: 319378

African (AFR) AF: 0.654 AC: 9589 AN: 14658

American (AMR) AF: 0.817 AC: 24201 AN: 29636

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 13590 AN: 18532

East Asian (EAS) AF: 0.713 AC: 24626 AN: 34536

South Asian (SAS) AF: 0.546 AC: 32964 AN: 60352

European-Finnish (FIN) AF: 0.794 AC: 40816 AN: 51412

Middle Eastern (MID) AF: 0.590 AC: 1444 AN: 2448

European-Non Finnish (NFE) AF: 0.711 AC: 245652 AN: 345708

Other (OTH) AF: 0.702 AC: 21483 AN: 30618

GnomAD4 genome AF: 0.685 AC: 104125 AN: 151936 Hom.: 36052 Cov.: 31 AF XY: 0.686 AC XY: 50923 AN XY: 74254

African (AFR) AF: 0.634 AC: 26227 AN: 41396

American (AMR) AF: 0.736 AC: 11249 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2530 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3266 AN: 5158

South Asian (SAS) AF: 0.591 AC: 2847 AN: 4816

European-Finnish (FIN) AF: 0.810 AC: 8538 AN: 10544

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47140 AN: 67952

Other (OTH) AF: 0.696 AC: 1468 AN: 2108

Alfa AF: 0.693 Hom.: 81051

Bravo AF: 0.685

Asia WGS AF: 0.633 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.41
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs9269081; hg19: chr6-32441100;