6-32460508-C-T

Variant names:

• chr6-32460508-C-T
• rs6903608
• ENST00000766009.1:n.201G>A

Variant summary

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

The ENST00000766009.1(ENSG00000299747):​n.201G>A 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 0.668 in 152,056 control chromosomes in the GnomAD database, including 34,257 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 0.67 (34257 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766009.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 115 publications found

Genes affected

ENSG00000299747 (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 = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766009.1. 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
	ENSG00000299747	ENST00000766009.1		n.201G>A		non_coding_transcript_exon	Exon 1 of 2
	HLA-DRB9	ENST00000449413.1	TSL:6	n.77-421G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101450 AN: 151938 Hom.: 34227 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.668 AC: 101523 AN: 152056 Hom.: 34257 Cov.: 32 AF XY: 0.668 AC XY: 49671 AN XY: 74336

African (AFR) AF: 0.613 AC: 25395 AN: 41434

American (AMR) AF: 0.706 AC: 10793 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2484 AN: 3472

East Asian (EAS) AF: 0.621 AC: 3208 AN: 5170

South Asian (SAS) AF: 0.577 AC: 2778 AN: 4816

European-Finnish (FIN) AF: 0.799 AC: 8451 AN: 10580

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46144 AN: 67980

Other (OTH) AF: 0.672 AC: 1420 AN: 2114

Alfa AF: 0.679 Hom.: 151582

Bravo AF: 0.666

Asia WGS AF: 0.598 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.9
DANN	Benign	0.66
PhyloP100		-0.27

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: rs6903608;

hg19: chr6-32428285;