8-86840704-T-G

Position:

• chr8-86840704-T-G

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 0.463 in 151,892 control chromosomes in the GnomAD database, including 16,520 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 0.46 (16520 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86840704T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70287 AN: 151774 Hom.: 16500 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.463 AC: 70359 AN: 151892 Hom.: 16520 Cov.: 32 AF XY: 0.469 AC XY: 34825 AN XY: 74232

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.435

Alfa AF: 0.455 Hom.: 2686

Bravo AF: 0.464

Asia WGS AF: 0.558 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.73
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1902866; hg19: chr8-87852932;