rs10052280

chr5-84601266-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 0.115 in 149,738 control chromosomes in the GnomAD database, including 1,444 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 0.11 (1444 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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: 0.115 AC: 17183 AN: 149708 Hom.: 1437 Cov.: 27

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0707

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0523

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.115 AC: 17212 AN: 149738 Hom.: 1444 Cov.: 27 AF XY: 0.116 AC XY: 8505 AN XY: 73054

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0707

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0306

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0559

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0664 Hom.: 879

Bravo AF: 0.127

Asia WGS AF: 0.100 AC: 347 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.6
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10052280; hg19: chr5-83897084;