6-32554612-T-G

Position:

• chr6-32554612-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000437183.5(HLA-DRB6):​n.831+7A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 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 0.76 (22872 hom., cov: 10)
  • Exomes 𝑓: 0.71 (114978 hom.)
  • Failed GnomAD Quality Control
• Consequence: HLA-DRB6 ENST00000437183.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

HLA-DRB6 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DRB6	NR_001298.1	n.740+78A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DRB6	ENST00000411500.5	n.740+78A>C		intron_variant		6
HLA-DRB6	ENST00000437183.5	n.831+7A>C		splice_region_variant, intron_variant		6
HLA-DRB6	ENST00000437650.2	n.553+78A>C		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.761 AC: 53066 AN: 69770 Hom.: 22844 Cov.: 10

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.897

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.813

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.715 AC: 269778 AN: 377464 Hom.: 114978 Cov.: 5 AF XY: 0.717 AC XY: 141646 AN XY: 197442

Gnomad4 AFR exome AF: 0.714

Gnomad4 AMR exome AF: 0.827

Gnomad4 ASJ exome AF: 0.878

Gnomad4 EAS exome AF: 0.694

Gnomad4 SAS exome AF: 0.680

Gnomad4 FIN exome AF: 0.789

Gnomad4 NFE exome AF: 0.702

Gnomad4 OTH exome AF: 0.707

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.761 AC: 53122 AN: 69846 Hom.: 22872 Cov.: 10 AF XY: 0.758 AC XY: 25673 AN XY: 33850

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.801

Alfa AF: 0.327 Hom.: 96

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36149991; hg19: chr6-32522389;