12-66036672-T-G

Variant names:

• chr12-66036672-T-G
• rs4130827

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 0.246 in 152,038 control chromosomes in the GnomAD database, including 5,293 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 0.25 (5293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 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: 0.246 AC: 37329 AN: 151920 Hom.: 5289 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.246 AC: 37345 AN: 152038 Hom.: 5293 Cov.: 32 AF XY: 0.248 AC XY: 18441 AN XY: 74308

African (AFR) AF: 0.114 AC: 4737 AN: 41520

American (AMR) AF: 0.383 AC: 5857 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3468

East Asian (EAS) AF: 0.140 AC: 722 AN: 5166

South Asian (SAS) AF: 0.358 AC: 1718 AN: 4800

European-Finnish (FIN) AF: 0.272 AC: 2869 AN: 10554

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19433 AN: 67934

Other (OTH) AF: 0.298 AC: 628 AN: 2108

Alfa AF: 0.288 Hom.: 3407

Bravo AF: 0.247

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs4130827; hg19: chr12-66430452;