12-90462864-A-G

Position:

• chr12-90462864-A-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 0.0231 in 152,222 control chromosomes in the GnomAD database, including 112 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 0.023 (112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0231 AC: 3516 AN: 152104 Hom.: 113 Cov.: 32

Gnomad AFR AF: 0.00562

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0526

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0575

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0231 AC: 3515 AN: 152222 Hom.: 112 Cov.: 32 AF XY: 0.0249 AC XY: 1849 AN XY: 74404

Gnomad4 AFR AF: 0.00560

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0576

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.0167

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0216 Hom.: 66

Bravo AF: 0.0259

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368009; hg19: chr12-90856641;