rs930506

Positions:

• chr10-52776791-T-C

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 0.306 in 151,988 control chromosomes in the GnomAD database, including 8,767 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 0.31 (8767 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46401 AN: 151870 Hom.: 8750 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.306 AC: 46454 AN: 151988 Hom.: 8767 Cov.: 31 AF XY: 0.301 AC XY: 22347 AN XY: 74294

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.279

Alfa AF: 0.251 Hom.: 2869

Bravo AF: 0.316

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs930506; hg19: chr10-54536551;