rs10490505

chr10-80759434-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 0.0351 in 152,288 control chromosomes in the GnomAD database, including 175 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 0.035 (175 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 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: 0.0351 AC: 5346 AN: 152170 Hom.: 174 Cov.: 33

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0351 AC: 5347 AN: 152288 Hom.: 175 Cov.: 33 AF XY: 0.0348 AC XY: 2592 AN XY: 74478

Gnomad4 AFR AF: 0.0792

Gnomad4 AMR AF: 0.0187

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0252

Gnomad4 NFE AF: 0.0193

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0328 Hom.: 25

Bravo AF: 0.0364

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.4
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490505; hg19: chr10-82519190;