rs10450310

Variant names:

• chr10-52764898-G-A
• rs10450310

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.416 AC: 17210 AN: 41386

American (AMR) AF: 0.230 AC: 3497 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3464

East Asian (EAS) AF: 0.172 AC: 888 AN: 5174

South Asian (SAS) AF: 0.201 AC: 965 AN: 4812

European-Finnish (FIN) AF: 0.251 AC: 2643 AN: 10514

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16205 AN: 67944

Other (OTH) AF: 0.279 AC: 589 AN: 2108

Alfa AF: 0.251 Hom.: 3302

Bravo AF: 0.287

Asia WGS AF: 0.203 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.22
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs10450310; hg19: chr10-54524658;