rs3116999

chr6-33129389-G-C

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 0.13 in 152,216 control chromosomes in the GnomAD database, including 1,469 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 0.13 (1469 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 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: 0.131 AC: 19851 AN: 152094 Hom.: 1473 Cov.: 31

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.0452

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.130 AC: 19861 AN: 152216 Hom.: 1469 Cov.: 31 AF XY: 0.130 AC XY: 9638 AN XY: 74418

Gnomad4 AFR AF: 0.0760

Gnomad4 AMR AF: 0.0949

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.116

Alfa AF: 0.152 Hom.: 984

Bravo AF: 0.120

Asia WGS AF: 0.144 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	7.4
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3116999; hg19: chr6-33097166;