12-66083192-T-C

Variant names:

• chr12-66083192-T-C
• rs11176031

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 0.322 in 152,136 control chromosomes in the GnomAD database, including 8,322 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 0.32 (8322 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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: 0.322 AC: 48931 AN: 152018 Hom.: 8304 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.322 AC: 48986 AN: 152136 Hom.: 8322 Cov.: 33 AF XY: 0.324 AC XY: 24118 AN XY: 74372

African (AFR) AF: 0.213 AC: 8838 AN: 41514

American (AMR) AF: 0.312 AC: 4767 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2706 AN: 5180

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4816

European-Finnish (FIN) AF: 0.350 AC: 3699 AN: 10556

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24749 AN: 68004

Other (OTH) AF: 0.357 AC: 754 AN: 2114

Alfa AF: 0.335 Hom.: 2333

Bravo AF: 0.317

Asia WGS AF: 0.416 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs11176031; hg19: chr12-66476972;