rs455707

Variant names:

• chr5-161186187-G-A
• rs455707

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 0.284 in 151,878 control chromosomes in the GnomAD database, including 7,721 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 0.28 (7721 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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: 0.284 AC: 43065 AN: 151760 Hom.: 7696 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.284 AC: 43141 AN: 151878 Hom.: 7721 Cov.: 31 AF XY: 0.282 AC XY: 20915 AN XY: 74214

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.277

Alfa AF: 0.208 Hom.: 6033

Bravo AF: 0.296

Asia WGS AF: 0.234 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs455707; hg19: chr5-160613194;