rs12406089

Variant names:

• chr1-11861124-C-G
• rs12406089

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 0.337 in 151,764 control chromosomes in the GnomAD database, including 8,908 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 0.34 (8908 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 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: 0.337 AC: 51147 AN: 151648 Hom.: 8885 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.337 AC: 51208 AN: 151764 Hom.: 8908 Cov.: 31 AF XY: 0.334 AC XY: 24777 AN XY: 74176

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.340

Alfa AF: 0.326 Hom.: 1085

Bravo AF: 0.333

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12406089; hg19: chr1-11921181; COSMIC: COSV64687432;