rs17725710

Variant names:

• chr10-125393113-A-G
• rs17725710

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 0.121 in 152,204 control chromosomes in the GnomAD database, including 1,502 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 0.12 (1502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 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: 0.121 AC: 18360 AN: 152086 Hom.: 1500 Cov.: 32

Gnomad AFR AF: 0.0265

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0758

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.121 AC: 18356 AN: 152204 Hom.: 1502 Cov.: 32 AF XY: 0.124 AC XY: 9261 AN XY: 74416

Gnomad4 AFR AF: 0.0264

Gnomad4 AMR AF: 0.0939

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0760

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.114

Alfa AF: 0.139 Hom.: 220

Bravo AF: 0.105

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.66
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17725710; hg19: chr10-127081682;