6-32553130-T-C

Position:

• chr6-32553130-T-C

Variant summary

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

The NR_001298.1(HLA-DRB6):​n.876-58A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 147,840 control chromosomes in the GnomAD database, including 39,141 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 0.71 (39141 hom., cov: 27)
  • Exomes 𝑓: 0.74 (89967 hom.)
  • Failed GnomAD Quality Control
• Consequence: HLA-DRB6 NR_001298.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

Genes affected

HLA-DRB6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DRB6	NR_001298.1	n.876-58A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DRB6	ENST00000411500.5	n.876-58A>G		intron_variant		6
HLA-DRB6	ENST00000437183.5	n.967-58A>G		intron_variant		6
HLA-DRB6	ENST00000437650.2	n.689-58A>G		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.715 AC: 105623 AN: 147724 Hom.: 39106 Cov.: 27

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.824

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.740

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.743 AC: 233993 AN: 314770 Hom.: 89967 AF XY: 0.749 AC XY: 131805 AN XY: 176052

Gnomad4 AFR exome AF: 0.751

Gnomad4 AMR exome AF: 0.832

Gnomad4 ASJ exome AF: 0.818

Gnomad4 EAS exome AF: 0.775

Gnomad4 SAS exome AF: 0.761

Gnomad4 FIN exome AF: 0.634

Gnomad4 NFE exome AF: 0.739

Gnomad4 OTH exome AF: 0.737

GnomAD4 genome AF: 0.715 AC: 105701 AN: 147840 Hom.: 39141 Cov.: 27 AF XY: 0.710 AC XY: 51081 AN XY: 71962

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.735

Alfa AF: 0.673 Hom.: 3878

Asia WGS AF: 0.657 AC: 2271 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.39
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3828840; hg19: chr6-32520907;