rs10080213

Variant names:

• chr5-53474149-A-G
• rs10080213

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 0.289 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.289 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

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.244

Alfa AF: 0.242 Hom.: 3133

Bravo AF: 0.295

Asia WGS AF: 0.293 AC: 1020 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10080213; hg19: chr5-52769979;