rs3128921

chr6-33102972-C-A

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 0.312 in 151,606 control chromosomes in the GnomAD database, including 8,126 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 (8126 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 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: 0.312 AC: 47198 AN: 151488 Hom.: 8103 Cov.: 29

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.312 AC: 47250 AN: 151606 Hom.: 8126 Cov.: 29 AF XY: 0.309 AC XY: 22880 AN XY: 74076

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.317

Alfa AF: 0.267 Hom.: 1907

Bravo AF: 0.314

Asia WGS AF: 0.403 AC: 1398 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.36
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3128921; hg19: chr6-33070749;