6-32460409-G-C

Variant names:

• chr6-32460409-G-C
• rs6923504
• ENST00000449413.1:n.77-322C>G

Variant summary

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

The ENST00000766009.1(ENSG00000299747):​n.219+81C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,984 control chromosomes in the GnomAD database, including 34,271 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 (34271 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 33 publications found

Genes affected

HLA-DRB9 (HGNC:4957): (major histocompatibility complex, class II, DR beta 9 (pseudogene))

ENSG00000299747 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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
	HLA-DRB9	ENST00000449413.1	TSL:6	n.77-322C>G		intron	N/A
	ENSG00000299747	ENST00000766009.1		n.219+81C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101434 AN: 151866 Hom.: 34241 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.625

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: 101507 AN: 151984 Hom.: 34271 Cov.: 31 AF XY: 0.668 AC XY: 49657 AN XY: 74286

African (AFR) AF: 0.613 AC: 25377 AN: 41428

American (AMR) AF: 0.706 AC: 10794 AN: 15280

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

East Asian (EAS) AF: 0.626 AC: 3231 AN: 5158

South Asian (SAS) AF: 0.577 AC: 2776 AN: 4812

European-Finnish (FIN) AF: 0.799 AC: 8443 AN: 10572

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

European-Non Finnish (NFE) AF: 0.679 AC: 46137 AN: 67950

Other (OTH) AF: 0.671 AC: 1415 AN: 2108

Alfa AF: 0.674 Hom.: 17408

Bravo AF: 0.666

Asia WGS AF: 0.604 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.39
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs6923504; hg19: chr6-32428186;