rs3117242

Variant names:

• chr6-33102116-A-G
• rs3117242

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.494 AC: 20495 AN: 41460

American (AMR) AF: 0.261 AC: 3984 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2928 AN: 5170

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4822

European-Finnish (FIN) AF: 0.250 AC: 2643 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18019 AN: 67984

Other (OTH) AF: 0.335 AC: 707 AN: 2110

Alfa AF: 0.293 Hom.: 11681

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs3117242; hg19: chr6-33069893;