10-52840206-A-G

Position:

• chr10-52840206-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 0.244 in 151,908 control chromosomes in the GnomAD database, including 4,658 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 0.24 (4658 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.326 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: 0.244 AC: 37071 AN: 151790 Hom.: 4649 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.244 AC: 37098 AN: 151908 Hom.: 4658 Cov.: 31 AF XY: 0.244 AC XY: 18148 AN XY: 74252

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.249

Alfa AF: 0.243 Hom.: 545

Bravo AF: 0.256

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10824815; hg19: chr10-54599966;