ENST00000449413.1:n.77-1147G>A

Variant names:

• chr6-32461234-C-T
• rs6919855
• ENST00000449413.1:n.77-1147G>A

Variant summary

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

The ENST00000449413.1(HLA-DRB9):​n.77-1147G>A 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 151,988 control chromosomes in the GnomAD database, including 34,237 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 (34237 hom., cov: 31)
• Consequence: HLA-DRB9 ENST00000449413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 20 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=-0.98).
• 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: ENST00000449413.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DRB9	ENST00000449413.1	TSL:6	n.77-1147G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101412 AN: 151870 Hom.: 34209 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.577

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: 101481 AN: 151988 Hom.: 34237 Cov.: 31 AF XY: 0.668 AC XY: 49664 AN XY: 74296

African (AFR) AF: 0.612 AC: 25367 AN: 41430

American (AMR) AF: 0.706 AC: 10776 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2481 AN: 3472

East Asian (EAS) AF: 0.626 AC: 3229 AN: 5162

South Asian (SAS) AF: 0.577 AC: 2781 AN: 4816

European-Finnish (FIN) AF: 0.799 AC: 8435 AN: 10554

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

European-Non Finnish (NFE) AF: 0.679 AC: 46144 AN: 67968

Other (OTH) AF: 0.671 AC: 1420 AN: 2116

Alfa AF: 0.732 Hom.: 14304

Bravo AF: 0.665

Asia WGS AF: 0.603 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs6919855; hg19: chr6-32429011;