rs10445323

Positions:

• chr17-58025592-A-G

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 0.197 in 152,162 control chromosomes in the GnomAD database, including 3,739 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 0.20 (3739 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29968 AN: 152044 Hom.: 3741 Cov.: 32

Gnomad AFR AF: 0.0635

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.197 AC: 29957 AN: 152162 Hom.: 3739 Cov.: 32 AF XY: 0.195 AC XY: 14533 AN XY: 74384

Gnomad4 AFR AF: 0.0633

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0834

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.242

Alfa AF: 0.250 Hom.: 2848

Bravo AF: 0.190

Asia WGS AF: 0.0440 AC: 156 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.5
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10445323; hg19: chr17-56102953;