rs10857452

Variant names:

• chr10-49261647-A-C
• rs10857452

Your query was ambiguous. Multiple possible variants found:

• chr10-49261647-A-C
• chr10-49261647-A-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0808 in 152,258 control chromosomes in the GnomAD database, including 591 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 0.081 (591 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.44
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.0809 AC: 12301 AN: 152140 Hom.: 590 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0659

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0808 AC: 12310 AN: 152258 Hom.: 591 Cov.: 33 AF XY: 0.0819 AC XY: 6100 AN XY: 74450

African (AFR) AF: 0.120 AC: 4982 AN: 41542

American (AMR) AF: 0.0463 AC: 709 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.0271 AC: 131 AN: 4830

European-Finnish (FIN) AF: 0.149 AC: 1581 AN: 10584

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0659 AC: 4483 AN: 68026

Other (OTH) AF: 0.0662 AC: 140 AN: 2114

Alfa AF: 0.0263 Hom.: 19

Bravo AF: 0.0745

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	22
DANN	Benign	0.83
PhyloP100		5.4

Splicing

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

Other links and lift over

dbSNP: rs10857452; hg19: chr10-50469692;