rs159782

Variant names:

• chr20-4366700-A-G
• rs159782

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 0.323 in 152,012 control chromosomes in the GnomAD database, including 8,087 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 0.32 (8087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665

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 (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49051 AN: 151894 Hom.: 8078 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.323 AC: 49086 AN: 152012 Hom.: 8087 Cov.: 32 AF XY: 0.323 AC XY: 24028 AN XY: 74308

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.320

Alfa AF: 0.307 Hom.: 981

Bravo AF: 0.320

Asia WGS AF: 0.343 AC: 1190 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	4.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159782; hg19: chr20-4347347;