rs930506

Variant names:

• chr10-52776791-T-C
• rs930506

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;