rs484458

Variant names:

• chr8-27627435-G-A
• rs484458

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 0.177 in 152,198 control chromosomes in the GnomAD database, including 2,870 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 (2870 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.859
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 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: 27011 AN: 152080 Hom.: 2871 Cov.: 33

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.177 AC: 27015 AN: 152198 Hom.: 2870 Cov.: 33 AF XY: 0.181 AC XY: 13440 AN XY: 74416

African (AFR) AF: 0.0571 AC: 2372 AN: 41548

American (AMR) AF: 0.177 AC: 2709 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 800 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1003 AN: 5172

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4820

European-Finnish (FIN) AF: 0.268 AC: 2836 AN: 10582

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.226 AC: 15385 AN: 67990

Other (OTH) AF: 0.193 AC: 409 AN: 2116

Alfa AF: 0.213 Hom.: 2359

Bravo AF: 0.166

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.73
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs484458; hg19: chr8-27484952;