12-90462864-A-G

Variant names:

• chr12-90462864-A-G
• rs1368009

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.00560 AC: 233 AN: 41574

American (AMR) AF: 0.0527 AC: 805 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3472

East Asian (EAS) AF: 0.146 AC: 751 AN: 5144

South Asian (SAS) AF: 0.0576 AC: 278 AN: 4828

European-Finnish (FIN) AF: 0.0133 AC: 141 AN: 10618

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0167 AC: 1136 AN: 67992

Other (OTH) AF: 0.0260 AC: 55 AN: 2114

Alfa AF: 0.0210 Hom.: 105

Bravo AF: 0.0259

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.38
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1368009; hg19: chr12-90856641;