chr20-60942423-A-G

Variant names:

• chr20-60942423-A-G
• rs6124036

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 0.0855 in 152,228 control chromosomes in the GnomAD database, including 1,757 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 0.085 (1757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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: 0.0853 AC: 12982 AN: 152110 Hom.: 1747 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0855 AC: 13015 AN: 152228 Hom.: 1757 Cov.: 32 AF XY: 0.0917 AC XY: 6829 AN XY: 74438

African (AFR) AF: 0.0965 AC: 4007 AN: 41538

American (AMR) AF: 0.255 AC: 3899 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3468

East Asian (EAS) AF: 0.599 AC: 3083 AN: 5144

South Asian (SAS) AF: 0.0569 AC: 274 AN: 4816

European-Finnish (FIN) AF: 0.0414 AC: 440 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0145 AC: 987 AN: 68030

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.0534 Hom.: 1794

Bravo AF: 0.110

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs6124036; hg19: chr20-59517479;