20-22790726-G-C

Variant names:

• chr20-22790726-G-C
• rs6048344

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 0.47 in 152,070 control chromosomes in the GnomAD database, including 19,016 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 0.47 (19016 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.470 AC: 71491 AN: 151952 Hom.: 19017 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.470 AC: 71491 AN: 152070 Hom.: 19016 Cov.: 33 AF XY: 0.470 AC XY: 34940 AN XY: 74344

African (AFR) AF: 0.216 AC: 8951 AN: 41468

American (AMR) AF: 0.591 AC: 9039 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2177 AN: 3470

East Asian (EAS) AF: 0.836 AC: 4325 AN: 5174

South Asian (SAS) AF: 0.429 AC: 2062 AN: 4808

European-Finnish (FIN) AF: 0.507 AC: 5359 AN: 10576

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37866 AN: 67970

Other (OTH) AF: 0.499 AC: 1055 AN: 2114

Alfa AF: 0.349 Hom.: 945

Bravo AF: 0.472

Asia WGS AF: 0.571 AC: 1985 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.75
DANN	Benign	0.64
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs6048344; hg19: chr20-22771364;