rs16929496

Variant names:

• chr12-25840870-T-C
• rs16929496

Your query was ambiguous. Multiple possible variants found:

• chr12-25840870-T-C
• chr12-25840870-T-G

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 0.189 in 151,818 control chromosomes in the GnomAD database, including 2,775 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 (2775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 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: 0.189 AC: 28732 AN: 151702 Hom.: 2777 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.189 AC: 28734 AN: 151818 Hom.: 2775 Cov.: 32 AF XY: 0.187 AC XY: 13898 AN XY: 74174

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.187

Alfa AF: 0.188 Hom.: 4282

Bravo AF: 0.187

Asia WGS AF: 0.183 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16929496; hg19: chr12-25993804;