chr20-23882207-G-A

Variant names:

• chr20-23882207-G-A
• rs6076157

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 0.568 in 151,970 control chromosomes in the GnomAD database, including 25,414 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 0.57 (25414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714
• 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 (NFE) allele frequency at 95% confidence interval = 0.655 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: 0.568 AC: 86252 AN: 151852 Hom.: 25410 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.568 AC: 86289 AN: 151970 Hom.: 25414 Cov.: 32 AF XY: 0.565 AC XY: 41990 AN XY: 74270

African (AFR) AF: 0.405 AC: 16781 AN: 41412

American (AMR) AF: 0.562 AC: 8590 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2440 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2687 AN: 5156

South Asian (SAS) AF: 0.628 AC: 3025 AN: 4820

European-Finnish (FIN) AF: 0.552 AC: 5838 AN: 10570

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.660 AC: 44856 AN: 67948

Other (OTH) AF: 0.619 AC: 1307 AN: 2112

Alfa AF: 0.627 Hom.: 50396

Bravo AF: 0.555

Asia WGS AF: 0.546 AC: 1894 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	7.9
DANN	Benign	0.65
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs6076157; hg19: chr20-23862844;