rs6066059

Positions:

• chr20-46739515-T-C
• chr20-46739515-T-G

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 0.248 in 151,994 control chromosomes in the GnomAD database, including 5,629 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 0.25 (5629 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46739515T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37762 AN: 151876 Hom.: 5627 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.248 AC: 37768 AN: 151994 Hom.: 5629 Cov.: 31 AF XY: 0.253 AC XY: 18784 AN XY: 74282

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.279

Alfa AF: 0.275 Hom.: 5871

Bravo AF: 0.243

Asia WGS AF: 0.375 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6066059; hg19: chr20-45368154;