rs10450310

Variant names:

• chr10-52764898-G-A
• rs10450310

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 0.284 in 151,834 control chromosomes in the GnomAD database, including 6,750 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 0.28 (6750 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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: 0.283 AC: 42990 AN: 151716 Hom.: 6735 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.284 AC: 43048 AN: 151834 Hom.: 6750 Cov.: 32 AF XY: 0.281 AC XY: 20881 AN XY: 74208

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.279

Alfa AF: 0.249 Hom.: 2812

Bravo AF: 0.287

Asia WGS AF: 0.203 AC: 708 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	1.0
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10450310; hg19: chr10-54524658;