12-90114532-G-T

Position:

• chr12-90114532-G-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 0.735 in 152,054 control chromosomes in the GnomAD database, including 41,958 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 0.74 (41958 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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: 0.735 AC: 111707 AN: 151936 Hom.: 41940 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.735 AC: 111771 AN: 152054 Hom.: 41958 Cov.: 31 AF XY: 0.741 AC XY: 55056 AN XY: 74322

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.745

Alfa AF: 0.783 Hom.: 20330

Bravo AF: 0.716

Asia WGS AF: 0.791 AC: 2752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777224; hg19: chr12-90508309;