rs10490505

Variant names:

• chr10-80759434-A-G
• rs10490505

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0792 AC: 3292 AN: 41540

American (AMR) AF: 0.0187 AC: 286 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4830

European-Finnish (FIN) AF: 0.0252 AC: 268 AN: 10622

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0193 AC: 1313 AN: 68024

Other (OTH) AF: 0.0331 AC: 70 AN: 2112

Alfa AF: 0.0238 Hom.: 88

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10490505; hg19: chr10-82519190;