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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0809 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

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0463

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0271

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.0659

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0216 Hom.: 11

Bravo AF: 0.0745

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10857452; hg19: chr10-50469692;