12-90462864-A-G

Variant names:

• chr12-90462864-A-G
• rs1368009

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;