6-32461234-C-T

Position:

• chr6-32461234-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32461234C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DRB9	ENST00000449413.1	n.77-1147G>A		intron_variant		6

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

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.671

Alfa AF: 0.559 Hom.: 1680

Bravo AF: 0.665

Asia WGS AF: 0.603 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6919855; hg19: chr6-32429011;