16-17645835-G-A

Variant names:

• chr16-17645835-G-A
• rs12445126

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 0.0892 in 152,202 control chromosomes in the GnomAD database, including 669 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 0.089 (669 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0936 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: 0.0892 AC: 13563 AN: 152084 Hom.: 670 Cov.: 33

Gnomad AFR AF: 0.0782

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0892 AC: 13574 AN: 152202 Hom.: 669 Cov.: 33 AF XY: 0.0893 AC XY: 6644 AN XY: 74408

African (AFR) AF: 0.0783 AC: 3250 AN: 41526

American (AMR) AF: 0.0817 AC: 1247 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.0731 AC: 379 AN: 5182

South Asian (SAS) AF: 0.0839 AC: 405 AN: 4826

European-Finnish (FIN) AF: 0.0891 AC: 945 AN: 10602

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6497 AN: 68006

Other (OTH) AF: 0.110 AC: 232 AN: 2112

Alfa AF: 0.0915 Hom.: 1322

Bravo AF: 0.0868

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.68
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs12445126; hg19: chr16-17739692;