20-43859616-A-C

Variant names:

• chr20-43859616-A-C
• rs6124601

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 0.285 in 152,098 control chromosomes in the GnomAD database, including 6,927 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 0.29 (6927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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: 0.285 AC: 43351 AN: 151980 Hom.: 6902 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.285 AC: 43423 AN: 152098 Hom.: 6927 Cov.: 32 AF XY: 0.293 AC XY: 21779 AN XY: 74354

African (AFR) AF: 0.372 AC: 15435 AN: 41452

American (AMR) AF: 0.323 AC: 4936 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2736 AN: 5182

South Asian (SAS) AF: 0.452 AC: 2179 AN: 4820

European-Finnish (FIN) AF: 0.175 AC: 1850 AN: 10596

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14618 AN: 67982

Other (OTH) AF: 0.286 AC: 605 AN: 2114

Alfa AF: 0.245 Hom.: 8069

Bravo AF: 0.298

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs6124601; hg19: chr20-42488256;