rs3128930

chr6-33107889-C-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 0.311 in 152,160 control chromosomes in the GnomAD database, including 8,270 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 0.31 (8270 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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: 0.311 AC: 47261 AN: 152042 Hom.: 8260 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.311 AC: 47289 AN: 152160 Hom.: 8270 Cov.: 33 AF XY: 0.305 AC XY: 22719 AN XY: 74398

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.297

Alfa AF: 0.257 Hom.: 6819

Bravo AF: 0.314

Asia WGS AF: 0.357 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.65
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3128930; hg19: chr6-33075666;