rs4518686

Variant names:

• chr8-125458575-A-G
• rs4518686

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 0.564 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.564 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

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.537

Alfa AF: 0.456 Hom.: 22575

Bravo AF: 0.584

Asia WGS AF: 0.762 AC: 2645 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	0.21
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4518686; hg19: chr8-126470817;