rs12926231

Variant names:

• chr16-16902859-A-G
• rs12926231

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 0.0556 in 152,192 control chromosomes in the GnomAD database, including 289 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 0.056 (289 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 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: 0.0557 AC: 8466 AN: 152074 Hom.: 289 Cov.: 31

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0629

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0556 AC: 8463 AN: 152192 Hom.: 289 Cov.: 31 AF XY: 0.0559 AC XY: 4161 AN XY: 74402

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.0431

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0632

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0572

Gnomad4 OTH AF: 0.0510

Alfa AF: 0.0553 Hom.: 35

Bravo AF: 0.0525

Asia WGS AF: 0.119 AC: 411 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12926231; hg19: chr16-16996716;