16-56959249-G-A

Variant names:

• chr16-56959249-G-A
• rs12149545

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 0.234 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
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0812 AC: 3369 AN: 41506

American (AMR) AF: 0.257 AC: 3923 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3470

East Asian (EAS) AF: 0.163 AC: 838 AN: 5152

South Asian (SAS) AF: 0.308 AC: 1480 AN: 4810

European-Finnish (FIN) AF: 0.273 AC: 2888 AN: 10560

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21346 AN: 67958

Other (OTH) AF: 0.227 AC: 478 AN: 2108

Alfa AF: 0.281 Hom.: 11054

Bravo AF: 0.226

Asia WGS AF: 0.200 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.79
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs12149545; hg19: chr16-56993161;