20-48461291-C-T

Variant names:

• chr20-48461291-C-T
• rs4458264

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 0.332 in 151,872 control chromosomes in the GnomAD database, including 8,751 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 (8751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 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: 0.331 AC: 50305 AN: 151754 Hom.: 8731 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.332 AC: 50365 AN: 151872 Hom.: 8751 Cov.: 32 AF XY: 0.340 AC XY: 25247 AN XY: 74192

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.312

Alfa AF: 0.319 Hom.: 999

Bravo AF: 0.341

Asia WGS AF: 0.414 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4458264; hg19: chr20-47089537;