rs459465

Variant names:

• chr20-54806483-G-A
• rs459465

Your query was ambiguous. Multiple possible variants found:

• chr20-54806483-G-A
• chr20-54806483-G-C
• chr20-54806483-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.150 AC: 6208 AN: 41422

American (AMR) AF: 0.160 AC: 2443 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3470

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5172

South Asian (SAS) AF: 0.108 AC: 520 AN: 4812

European-Finnish (FIN) AF: 0.234 AC: 2448 AN: 10476

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14218 AN: 67968

Other (OTH) AF: 0.179 AC: 376 AN: 2106

Alfa AF: 0.193 Hom.: 8871

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs459465; hg19: chr20-53423022;