chr20-23597552-G-A

Variant names:

• chr20-23597552-G-A
• rs1158167

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 0.722 in 152,014 control chromosomes in the GnomAD database, including 40,643 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 0.72 (40643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109674 AN: 151896 Hom.: 40619 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.722 AC: 109737 AN: 152014 Hom.: 40643 Cov.: 32 AF XY: 0.724 AC XY: 53803 AN XY: 74310

African (AFR) AF: 0.552 AC: 22859 AN: 41416

American (AMR) AF: 0.826 AC: 12617 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2761 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4595 AN: 5174

South Asian (SAS) AF: 0.693 AC: 3338 AN: 4814

European-Finnish (FIN) AF: 0.768 AC: 8122 AN: 10570

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52808 AN: 67982

Other (OTH) AF: 0.743 AC: 1567 AN: 2110

Alfa AF: 0.766 Hom.: 177343

Bravo AF: 0.723

Asia WGS AF: 0.806 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.70
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs1158167; hg19: chr20-23578189;