rs3809566

Variant names:

• chr15-63041525-A-G
• rs3809566

Your query was ambiguous. Multiple possible variants found:

• chr15-63041525-A-G
• chr15-63041525-A-T

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 0.683 in 152,124 control chromosomes in the GnomAD database, including 35,600 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 0.68 (35600 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.737 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: 0.683 AC: 103798 AN: 152006 Hom.: 35564 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.683 AC: 103877 AN: 152124 Hom.: 35600 Cov.: 33 AF XY: 0.679 AC XY: 50517 AN XY: 74382

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.682

Alfa AF: 0.676 Hom.: 4696

Bravo AF: 0.692

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809566; hg19: chr15-63333724;