rs1569723

Positions:

• chr20-46113425-C-A

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 0.792 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.767

Alfa AF: 0.749 Hom.: 94934

Bravo AF: 0.803

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1569723; hg19: chr20-44742064;