chr8-83587306-A-G

Variant names:

• chr8-83587306-A-G
• rs2220456

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 0.279 in 151,678 control chromosomes in the GnomAD database, including 6,539 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 0.28 (6539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42285 AN: 151560 Hom.: 6515 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.279 AC: 42372 AN: 151678 Hom.: 6539 Cov.: 32 AF XY: 0.277 AC XY: 20523 AN XY: 74104

African (AFR) AF: 0.417 AC: 17224 AN: 41354

American (AMR) AF: 0.266 AC: 4032 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3462

East Asian (EAS) AF: 0.186 AC: 960 AN: 5156

South Asian (SAS) AF: 0.184 AC: 887 AN: 4828

European-Finnish (FIN) AF: 0.234 AC: 2465 AN: 10534

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15622 AN: 67852

Other (OTH) AF: 0.254 AC: 534 AN: 2102

Alfa AF: 0.230 Hom.: 6607

Bravo AF: 0.292

Asia WGS AF: 0.207 AC: 717 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.76
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2220456; hg19: chr8-84499541;