rs6066724

Variant names:

• chr20-48389695-G-A
• rs6066724

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0658

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.0507

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.169

Alfa AF: 0.253 Hom.: 2905

Bravo AF: 0.183

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6066724; hg19: chr20-47018438;