rs459465

Positions:

• chr20-54806483-G-A

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 0.178 in 151,880 control chromosomes in the GnomAD database, including 2,547 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 0.18 (2547 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

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 (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27039 AN: 151762 Hom.: 2548 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.178 AC: 27046 AN: 151880 Hom.: 2547 Cov.: 31 AF XY: 0.178 AC XY: 13193 AN XY: 74200

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.179

Alfa AF: 0.199 Hom.: 4135

Bravo AF: 0.170

Asia WGS AF: 0.0700 AC: 244 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	0.12
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: rs459465; hg19: chr20-53423022;