rs1569723

Variant names:

• chr20-46113425-C-A
• rs1569723

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 0.792 in 152,232 control chromosomes in the GnomAD database, including 48,560 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 0.79 (48560 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 106 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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: 0.792 AC: 120499 AN: 152114 Hom.: 48486 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.792 AC: 120634 AN: 152232 Hom.: 48560 Cov.: 32 AF XY: 0.787 AC XY: 58564 AN XY: 74410

African (AFR) AF: 0.939 AC: 39047 AN: 41568

American (AMR) AF: 0.776 AC: 11860 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2534 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2928 AN: 5170

South Asian (SAS) AF: 0.737 AC: 3556 AN: 4828

European-Finnish (FIN) AF: 0.723 AC: 7651 AN: 10588

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50533 AN: 67998

Other (OTH) AF: 0.767 AC: 1622 AN: 2116

Alfa AF: 0.758 Hom.: 196313

Bravo AF: 0.803

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.56
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1569723; hg19: chr20-44742064;