rs9859392

chr3-41193025-C-Gchr3-41193025-C-T

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 0.392 in 151,978 control chromosomes in the GnomAD database, including 12,157 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 0.39 (12157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.392 AC: 59550 AN: 151860 Hom.: 12152 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.392 AC: 59579 AN: 151978 Hom.: 12157 Cov.: 32 AF XY: 0.389 AC XY: 28892 AN XY: 74266

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.385

Alfa AF: 0.405 Hom.: 1596

Bravo AF: 0.381

Asia WGS AF: 0.360 AC: 1254 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.59
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9859392; hg19: chr3-41234516;