rs10762810

chr10-78821014-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 0.293 in 152,208 control chromosomes in the GnomAD database, including 7,216 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 (7216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 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: 0.293 AC: 44632 AN: 152090 Hom.: 7214 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.293 AC: 44651 AN: 152208 Hom.: 7216 Cov.: 32 AF XY: 0.294 AC XY: 21846 AN XY: 74418

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.300

Alfa AF: 0.349 Hom.: 5511

Bravo AF: 0.282

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	8.5
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10762810; hg19: chr10-80580771;