rs4518686

Variant names:

• chr8-125458575-A-G
• rs4518686

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 0.564 in 152,156 control chromosomes in the GnomAD database, including 26,751 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 0.56 (26751 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85709 AN: 152038 Hom.: 26709 Cov.: 33

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.564 AC: 85814 AN: 152156 Hom.: 26751 Cov.: 33 AF XY: 0.573 AC XY: 42642 AN XY: 74376

African (AFR) AF: 0.797 AC: 33108 AN: 41530

American (AMR) AF: 0.604 AC: 9231 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3468

East Asian (EAS) AF: 0.841 AC: 4362 AN: 5186

South Asian (SAS) AF: 0.741 AC: 3570 AN: 4818

European-Finnish (FIN) AF: 0.430 AC: 4542 AN: 10572

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27658 AN: 67984

Other (OTH) AF: 0.537 AC: 1135 AN: 2114

Alfa AF: 0.466 Hom.: 30067

Bravo AF: 0.584

Asia WGS AF: 0.762 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.61
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4518686; hg19: chr8-126470817;