rs12445126

chr16-17645835-G-Achr16-17645835-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;