chr8-83220780-A-T

Position:

• chr8-83220780-A-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 0.9 in 151,978 control chromosomes in the GnomAD database, including 62,095 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 0.90 (62095 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.83220780A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136698 AN: 151860 Hom.: 62068 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.900 AC: 136778 AN: 151978 Hom.: 62095 Cov.: 32 AF XY: 0.900 AC XY: 66859 AN XY: 74322

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.915

Alfa AF: 0.940 Hom.: 3268

Bravo AF: 0.887

Asia WGS AF: 0.877 AC: 3048 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.48
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2140014; hg19: chr8-84133015;