rs10080213

Variant names:

• chr5-53474149-A-G
• rs10080213

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 0.289 in 152,082 control chromosomes in the GnomAD database, including 7,195 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 0.29 (7195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43862 AN: 151966 Hom.: 7175 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.289 AC: 43925 AN: 152082 Hom.: 7195 Cov.: 32 AF XY: 0.287 AC XY: 21315 AN XY: 74344

African (AFR) AF: 0.458 AC: 18992 AN: 41476

American (AMR) AF: 0.227 AC: 3470 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3470

East Asian (EAS) AF: 0.176 AC: 913 AN: 5186

South Asian (SAS) AF: 0.333 AC: 1607 AN: 4820

European-Finnish (FIN) AF: 0.232 AC: 2458 AN: 10582

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15021 AN: 67954

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.239 Hom.: 4187

Bravo AF: 0.295

Asia WGS AF: 0.293 AC: 1020 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.52
DANN	Benign	0.75
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs10080213; hg19: chr5-52769979;