20-46739515-T-C

Variant names:

• chr20-46739515-T-C
• rs6066059

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;