rs10445323

Variant names:

• chr17-58025592-A-G
• rs10445323

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 0.197 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0633 AC: 2631 AN: 41540

American (AMR) AF: 0.219 AC: 3353 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0834 AC: 403 AN: 4830

European-Finnish (FIN) AF: 0.281 AC: 2973 AN: 10564

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18738 AN: 67974

Other (OTH) AF: 0.242 AC: 513 AN: 2116

Alfa AF: 0.251 Hom.: 3124

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10445323; hg19: chr17-56102953;