rs12149545

chr16-56959249-G-A

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 0.234 in 152,044 control chromosomes in the GnomAD database, including 4,989 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 0.23 (4989 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35611 AN: 151926 Hom.: 4990 Cov.: 31

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.234 AC: 35605 AN: 152044 Hom.: 4989 Cov.: 31 AF XY: 0.233 AC XY: 17351 AN XY: 74312

Gnomad4 AFR AF: 0.0812

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.227

Alfa AF: 0.280 Hom.: 1389

Bravo AF: 0.226

Asia WGS AF: 0.200 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.6
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12149545; hg19: chr16-56993161;