6-84255564-T-C

Position:

• chr6-84255564-T-C

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 0.779 in 152,164 control chromosomes in the GnomAD database, including 46,280 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 0.78 (46280 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84255564T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118417 AN: 152046 Hom.: 46226 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.779 AC: 118530 AN: 152164 Hom.: 46280 Cov.: 33 AF XY: 0.777 AC XY: 57803 AN XY: 74376

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.750

Alfa AF: 0.770 Hom.: 86603

Bravo AF: 0.783

Asia WGS AF: 0.718 AC: 2492 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.030
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324089; hg19: chr6-84965282;