8-83220780-A-T

Variant names:

• chr8-83220780-A-T
• rs2140014

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.783 AC: 32472 AN: 41460

American (AMR) AF: 0.871 AC: 13293 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3244 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4418 AN: 5158

South Asian (SAS) AF: 0.939 AC: 4529 AN: 4822

European-Finnish (FIN) AF: 0.966 AC: 10232 AN: 10590

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65473 AN: 67904

Other (OTH) AF: 0.915 AC: 1931 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.48
DANN	Benign	0.14
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2140014; hg19: chr8-84133015;