rs12921716

Variant names:

• chr16-69520978-G-A
• rs12921716

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 0.0579 in 152,226 control chromosomes in the GnomAD database, including 399 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 0.058 (399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0862 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: 0.0580 AC: 8817 AN: 152108 Hom.: 399 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0278

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0579 AC: 8813 AN: 152226 Hom.: 399 Cov.: 32 AF XY: 0.0567 AC XY: 4217 AN XY: 74424

Gnomad4 AFR AF: 0.0139

Gnomad4 AMR AF: 0.0468

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.0732

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.0664

Alfa AF: 0.0787 Hom.: 309

Bravo AF: 0.0546

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12921716; hg19: chr16-69554881;