6-32461817-A-G

Variant names:

• chr6-32461817-A-G
• rs9268852
• ENST00000449413.1:n.77-1730T>C

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-1730T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,070 control chromosomes in the GnomAD database, including 25,451 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 0.58 (25451 hom., cov: 33)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 17 publications found

Genes affected

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.621 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DRB9	ENST00000449413.1	TSL:6	n.77-1730T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87679 AN: 151952 Hom.: 25432 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.596

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.577 AC: 87738 AN: 152070 Hom.: 25451 Cov.: 33 AF XY: 0.574 AC XY: 42643 AN XY: 74336

African (AFR) AF: 0.568 AC: 23533 AN: 41456

American (AMR) AF: 0.631 AC: 9643 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2341 AN: 3468

East Asian (EAS) AF: 0.591 AC: 3050 AN: 5164

South Asian (SAS) AF: 0.495 AC: 2390 AN: 4824

European-Finnish (FIN) AF: 0.589 AC: 6227 AN: 10566

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38670 AN: 68004

Other (OTH) AF: 0.591 AC: 1250 AN: 2114

Alfa AF: 0.564 Hom.: 16912

Bravo AF: 0.588

Asia WGS AF: 0.529 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.73
PhyloP100		-0.89

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9268852;

hg19: chr6-32429594;