rs12933929

Variant names:

• chr16-35877214-G-A
• rs12933929

Your query was ambiguous. Multiple possible variants found:

• chr16-35877214-G-A
• chr16-35877214-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 0.329 in 151,984 control chromosomes in the GnomAD database, including 10,221 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 0.33 (10221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 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: 0.329 AC: 49929 AN: 151866 Hom.: 10218 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.329 AC: 49942 AN: 151984 Hom.: 10221 Cov.: 32 AF XY: 0.322 AC XY: 23924 AN XY: 74288

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.0951

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.354

Alfa AF: 0.279 Hom.: 1291

Bravo AF: 0.327

Asia WGS AF: 0.146 AC: 510 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12933929; hg19: chr16-35111585;