12-90962263-T-G

Position:

• chr12-90962263-T-G

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 0.718 in 152,034 control chromosomes in the GnomAD database, including 41,226 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 0.72 (41226 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 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: 0.718 AC: 109135 AN: 151916 Hom.: 41223 Cov.: 31

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.718 AC: 109160 AN: 152034 Hom.: 41226 Cov.: 31 AF XY: 0.720 AC XY: 53527 AN XY: 74336

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.750

Alfa AF: 0.736 Hom.: 4343

Bravo AF: 0.698

Asia WGS AF: 0.725 AC: 2521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12820238; hg19: chr12-91356040;