rs12926729

Variant names:

• chr16-20089048-G-A
• rs12926729

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 0.194 in 152,112 control chromosomes in the GnomAD database, including 3,437 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 0.19 (3437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

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 (EAS) allele frequency at 95% confidence interval = 0.255 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: 0.194 AC: 29478 AN: 151994 Hom.: 3439 Cov.: 32

Gnomad AFR AF: 0.0602

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.194 AC: 29479 AN: 152112 Hom.: 3437 Cov.: 32 AF XY: 0.197 AC XY: 14650 AN XY: 74348

Gnomad4 AFR AF: 0.0601

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.184

Alfa AF: 0.222 Hom.: 558

Bravo AF: 0.183

Asia WGS AF: 0.224 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12926729; hg19: chr16-20100370;