rs12924103

Variant names:

• chr16-20083224-T-C
• rs12924103

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 0.219 in 151,786 control chromosomes in the GnomAD database, including 3,860 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 0.22 (3860 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.917

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.219 AC: 33257 AN: 151666 Hom.: 3861 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.219 AC: 33272 AN: 151786 Hom.: 3860 Cov.: 31 AF XY: 0.222 AC XY: 16469 AN XY: 74182

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.210

Alfa AF: 0.240 Hom.: 719

Bravo AF: 0.213

Asia WGS AF: 0.231 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12924103; hg19: chr16-20094546;