rs3117226

chr6-33089882-G-A

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 0.327 in 151,830 control chromosomes in the GnomAD database, including 9,308 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 0.33 (9308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 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: 0.327 AC: 49611 AN: 151708 Hom.: 9286 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.327 AC: 49666 AN: 151830 Hom.: 9308 Cov.: 32 AF XY: 0.322 AC XY: 23910 AN XY: 74194

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.324

Alfa AF: 0.264 Hom.: 8446

Bravo AF: 0.334

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.65
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117226; hg19: chr6-33057659;