3-41193025-C-G

Variant names:

• chr3-41193025-C-G
• rs9859392

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;