rs1158167

Positions:

• chr20-23597552-G-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 0.722 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.722 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

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.743

Alfa AF: 0.774 Hom.: 81781

Bravo AF: 0.723

Asia WGS AF: 0.806 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1158167; hg19: chr20-23578189;