rs455707

Variant names:

• chr5-161186187-G-A
• rs455707

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 0.284 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.508 AC: 21007 AN: 41358

American (AMR) AF: 0.203 AC: 3101 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1098 AN: 3464

East Asian (EAS) AF: 0.199 AC: 1024 AN: 5140

South Asian (SAS) AF: 0.248 AC: 1190 AN: 4806

European-Finnish (FIN) AF: 0.195 AC: 2064 AN: 10570

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.189 AC: 12833 AN: 67964

Other (OTH) AF: 0.277 AC: 584 AN: 2108

Alfa AF: 0.220 Hom.: 16838

Bravo AF: 0.296

Asia WGS AF: 0.234 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs455707; hg19: chr5-160613194;