rs12924103

Variant names:

• chr16-20083224-T-C
• rs12924103

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 0.219 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.138 AC: 5738 AN: 41436

American (AMR) AF: 0.234 AC: 3561 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3464

East Asian (EAS) AF: 0.268 AC: 1375 AN: 5138

South Asian (SAS) AF: 0.232 AC: 1110 AN: 4780

European-Finnish (FIN) AF: 0.299 AC: 3152 AN: 10526

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16871 AN: 67894

Other (OTH) AF: 0.210 AC: 440 AN: 2100

Alfa AF: 0.234 Hom.: 1444

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
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs12924103; hg19: chr16-20094546;