12-90463160-A-T

Variant names:

• chr12-90463160-A-T
• rs844102

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 0.52 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.843 AC: 34925 AN: 41438

American (AMR) AF: 0.469 AC: 7145 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 979 AN: 3462

East Asian (EAS) AF: 0.688 AC: 3518 AN: 5114

South Asian (SAS) AF: 0.444 AC: 2137 AN: 4812

European-Finnish (FIN) AF: 0.337 AC: 3535 AN: 10502

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25204 AN: 67858

Other (OTH) AF: 0.460 AC: 965 AN: 2096

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs844102; hg19: chr12-90856937;