rs2220456

Variant names:

• chr8-83587306-A-G
• rs2220456

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 0.279 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.254

Alfa AF: 0.228 Hom.: 5475

Bravo AF: 0.292

Asia WGS AF: 0.207 AC: 717 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2220456; hg19: chr8-84499541;