12-11630577-C-T

Variant names:

• chr12-11630577-C-T
• rs7312834

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 0.828 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.630 AC: 26114 AN: 41448

American (AMR) AF: 0.924 AC: 14135 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3198 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4326 AN: 5174

South Asian (SAS) AF: 0.912 AC: 4394 AN: 4818

European-Finnish (FIN) AF: 0.872 AC: 9222 AN: 10580

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61644 AN: 68020

Other (OTH) AF: 0.860 AC: 1815 AN: 2110

Alfa AF: 0.891 Hom.: 228682

Bravo AF: 0.824

Asia WGS AF: 0.876 AC: 3045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.59
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7312834; hg19: chr12-11783511;