rs12406089

chr1-11861124-C-G

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/exons	MANE	UniProt

Ensembl

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