rs3128930

Variant names:

• chr6-33107889-C-T
• rs3128930

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;