rs484458

Positions:

• chr8-27627435-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 0.177 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0571

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.193

Alfa AF: 0.212 Hom.: 2184

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs484458; hg19: chr8-27484952;