rs6066724

Variant names:

• chr20-48389695-G-A
• rs6066724

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 0.191 in 152,208 control chromosomes in the GnomAD database, including 3,616 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 0.19 (3616 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.60
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29042 AN: 152090 Hom.: 3616 Cov.: 33

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.191 AC: 29057 AN: 152208 Hom.: 3616 Cov.: 33 AF XY: 0.184 AC XY: 13727 AN XY: 74420

African (AFR) AF: 0.0658 AC: 2734 AN: 41550

American (AMR) AF: 0.148 AC: 2267 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3470

East Asian (EAS) AF: 0.0507 AC: 263 AN: 5190

South Asian (SAS) AF: 0.195 AC: 938 AN: 4820

European-Finnish (FIN) AF: 0.192 AC: 2032 AN: 10578

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19396 AN: 67994

Other (OTH) AF: 0.169 AC: 357 AN: 2114

Alfa AF: 0.247 Hom.: 3884

Bravo AF: 0.183

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.57
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs6066724; hg19: chr20-47018438;