rs10490505

Variant names:

• chr10-80759434-A-G
• rs10490505

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;