rs3117242

Variant names:

• chr6-33102116-A-G
• rs3117242

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 0.334 in 152,092 control chromosomes in the GnomAD database, including 9,591 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 (9591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 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: 0.334 AC: 50797 AN: 151972 Hom.: 9567 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.334 AC: 50851 AN: 152092 Hom.: 9591 Cov.: 32 AF XY: 0.330 AC XY: 24523 AN XY: 74330

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.335

Alfa AF: 0.280 Hom.: 1677

Bravo AF: 0.339

Asia WGS AF: 0.400 AC: 1388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117242; hg19: chr6-33069893;