12-11630577-C-T

Position:

• chr12-11630577-C-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 0.828 in 152,130 control chromosomes in the GnomAD database, including 53,323 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 0.83 (53323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125937 AN: 152012 Hom.: 53299 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.828 AC: 126004 AN: 152130 Hom.: 53323 Cov.: 32 AF XY: 0.829 AC XY: 61646 AN XY: 74360

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.860

Alfa AF: 0.903 Hom.: 119190

Bravo AF: 0.824

Asia WGS AF: 0.876 AC: 3045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7312834; hg19: chr12-11783511;