rs589686

Variant names:

• chr8-114976244-T-C
• rs589686

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 0.366 in 152,006 control chromosomes in the GnomAD database, including 11,142 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 0.37 (11142 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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: 0.366 AC: 55529 AN: 151888 Hom.: 11117 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.366 AC: 55604 AN: 152006 Hom.: 11142 Cov.: 33 AF XY: 0.366 AC XY: 27230 AN XY: 74302

African (AFR) AF: 0.548 AC: 22717 AN: 41432

American (AMR) AF: 0.277 AC: 4229 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1538 AN: 5172

South Asian (SAS) AF: 0.292 AC: 1410 AN: 4826

European-Finnish (FIN) AF: 0.338 AC: 3579 AN: 10574

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20167 AN: 67934

Other (OTH) AF: 0.319 AC: 675 AN: 2114

Alfa AF: 0.348 Hom.: 1316

Bravo AF: 0.363

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs589686; hg19: chr8-115988473;