rs9423593

Variant names:

• chr10-5290386-C-T
• rs9423593

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 0.29 in 152,070 control chromosomes in the GnomAD database, including 7,248 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 0.29 (7248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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: 0.290 AC: 44109 AN: 151952 Hom.: 7244 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.290 AC: 44122 AN: 152070 Hom.: 7248 Cov.: 32 AF XY: 0.287 AC XY: 21318 AN XY: 74326

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.319

Alfa AF: 0.321 Hom.: 1422

Bravo AF: 0.282

Asia WGS AF: 0.143 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9423593; hg19: chr10-5332349;