rs6063454

Variant names:

• chr20-49974254-G-T
• rs6063454

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 0.329 in 152,062 control chromosomes in the GnomAD database, including 9,765 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 0.33 (9765 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 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: 0.329 AC: 50035 AN: 151944 Hom.: 9758 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.329 AC: 50066 AN: 152062 Hom.: 9765 Cov.: 32 AF XY: 0.342 AC XY: 25397 AN XY: 74326

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.342

Alfa AF: 0.385 Hom.: 1871

Bravo AF: 0.294

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6063454; hg19: chr20-48590791;