chr20-23043282-A-G

Position:

• chr20-23043282-A-G

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 0.337 in 152,180 control chromosomes in the GnomAD database, including 8,861 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 0.34 (8861 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

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 (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51212 AN: 152062 Hom.: 8867 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.337 AC: 51225 AN: 152180 Hom.: 8861 Cov.: 33 AF XY: 0.339 AC XY: 25242 AN XY: 74406

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.354

Alfa AF: 0.335 Hom.: 1691

Bravo AF: 0.327

Asia WGS AF: 0.368 AC: 1278 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	3.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6082986; hg19: chr20-23023919;