rs3117225

chr6-33089934-G-Achr6-33089934-G-T

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 0.384 in 152,054 control chromosomes in the GnomAD database, including 12,715 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 0.38 (12715 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 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: 0.383 AC: 58264 AN: 151936 Hom.: 12692 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.384 AC: 58316 AN: 152054 Hom.: 12715 Cov.: 32 AF XY: 0.377 AC XY: 28032 AN XY: 74350

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.397

Alfa AF: 0.316 Hom.: 5007

Bravo AF: 0.393

Asia WGS AF: 0.489 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.1
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117225; hg19: chr6-33057711;