rs12445126

Variant names:

• chr16-17645835-G-A
• rs12445126

Your query was ambiguous. Multiple possible variants found:

• chr16-17645835-G-A
• chr16-17645835-G-T

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 0.0892 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0892 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

Gnomad4 AFR AF: 0.0783

Gnomad4 AMR AF: 0.0817

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.0839

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.0955

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0917 Hom.: 362

Bravo AF: 0.0868

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12445126; hg19: chr16-17739692;