rs3799369

chr6-25912406-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 0.075 in 152,244 control chromosomes in the GnomAD database, including 531 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 0.075 (531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0751 AC: 11429 AN: 152126 Hom.: 533 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.0945

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0750 AC: 11420 AN: 152244 Hom.: 531 Cov.: 32 AF XY: 0.0742 AC XY: 5523 AN XY: 74438

Gnomad4 AFR AF: 0.0206

Gnomad4 AMR AF: 0.0779

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.0795

Gnomad4 FIN AF: 0.0945

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.100 Hom.: 1038

Bravo AF: 0.0716

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.39
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3799369; hg19: chr6-25912634;