rs1566869

Variant names:

• chr12-51872564-G-A
• rs1566869

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 0.246 in 152,018 control chromosomes in the GnomAD database, including 5,811 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 0.25 (5811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 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: 0.246 AC: 37372 AN: 151900 Hom.: 5788 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.246 AC: 37433 AN: 152018 Hom.: 5811 Cov.: 32 AF XY: 0.259 AC XY: 19270 AN XY: 74304

African (AFR) AF: 0.195 AC: 8095 AN: 41464

American (AMR) AF: 0.405 AC: 6186 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3470

East Asian (EAS) AF: 0.710 AC: 3662 AN: 5160

South Asian (SAS) AF: 0.423 AC: 2032 AN: 4806

European-Finnish (FIN) AF: 0.273 AC: 2883 AN: 10554

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13026 AN: 67982

Other (OTH) AF: 0.240 AC: 507 AN: 2110

Alfa AF: 0.223 Hom.: 8267

Bravo AF: 0.255

Asia WGS AF: 0.568 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1566869; hg19: chr12-52266348;