rs3128921

Variant names:

• chr6-33102972-C-A
• rs3128921

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.430 AC: 17772 AN: 41316

American (AMR) AF: 0.249 AC: 3802 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 458 AN: 3456

East Asian (EAS) AF: 0.571 AC: 2941 AN: 5152

South Asian (SAS) AF: 0.281 AC: 1349 AN: 4800

European-Finnish (FIN) AF: 0.244 AC: 2548 AN: 10426

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17533 AN: 67902

Other (OTH) AF: 0.317 AC: 664 AN: 2096

Alfa AF: 0.272 Hom.: 6309

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs3128921; hg19: chr6-33070749;