12-90463160-A-T

Position:

• chr12-90463160-A-T

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 0.52 in 151,716 control chromosomes in the GnomAD database, including 23,983 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 0.52 (23983 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.90463160A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78760 AN: 151598 Hom.: 23931 Cov.: 31

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.520 AC: 78873 AN: 151716 Hom.: 23983 Cov.: 31 AF XY: 0.516 AC XY: 38224 AN XY: 74102

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.460

Alfa AF: 0.246 Hom.: 496

Bravo AF: 0.543

Asia WGS AF: 0.637 AC: 2212 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.018
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844102; hg19: chr12-90856937;