rs10080213

chr5-53474149-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;