rs12149545

Variant names:

• chr16-56959249-G-A
• rs12149545

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;