chr20-4366700-A-G

Variant names:

• chr20-4366700-A-G
• rs159782

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 0.323 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
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.383 AC: 15865 AN: 41450

American (AMR) AF: 0.255 AC: 3898 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1237 AN: 3460

East Asian (EAS) AF: 0.375 AC: 1932 AN: 5158

South Asian (SAS) AF: 0.328 AC: 1578 AN: 4816

European-Finnish (FIN) AF: 0.310 AC: 3276 AN: 10580

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.296 AC: 20145 AN: 67962

Other (OTH) AF: 0.320 AC: 675 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.64
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs159782; hg19: chr20-4347347;