rs1566080

Positions:

• chr8-141546705-A-C
• chr8-141546705-A-G
• chr8-141546705-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 0.616 in 151,438 control chromosomes in the GnomAD database, including 29,048 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 0.62 (29048 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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 = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93251 AN: 151322 Hom.: 29011 Cov.: 29

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.616 AC: 93335 AN: 151438 Hom.: 29048 Cov.: 29 AF XY: 0.622 AC XY: 45994 AN XY: 73946

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.611

Alfa AF: 0.574 Hom.: 40082

Bravo AF: 0.622

Asia WGS AF: 0.702 AC: 2442 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	2.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1566080; hg19: chr8-142556805;