chr20-4190850-A-G

Variant names:

• chr20-4190850-A-G
• rs6084657

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 0.426 in 152,132 control chromosomes in the GnomAD database, including 14,477 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 0.43 (14477 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 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: 0.426 AC: 64764 AN: 152014 Hom.: 14479 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.426 AC: 64767 AN: 152132 Hom.: 14477 Cov.: 33 AF XY: 0.426 AC XY: 31662 AN XY: 74388

African (AFR) AF: 0.299 AC: 12396 AN: 41510

American (AMR) AF: 0.480 AC: 7339 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1873 AN: 5168

South Asian (SAS) AF: 0.316 AC: 1526 AN: 4824

European-Finnish (FIN) AF: 0.512 AC: 5426 AN: 10590

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33038 AN: 67970

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.466 Hom.: 72896

Bravo AF: 0.420

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.74
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs6084657; hg19: chr20-4171497; COSMIC: COSV53868677;