12-91126079-C-T

Variant names:

• chr12-91126079-C-T
• rs12819853

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 0.192 in 152,184 control chromosomes in the GnomAD database, including 3,668 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 0.19 (3668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.268 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: 0.193 AC: 29289 AN: 152062 Hom.: 3669 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.192 AC: 29284 AN: 152184 Hom.: 3668 Cov.: 32 AF XY: 0.194 AC XY: 14430 AN XY: 74380

African (AFR) AF: 0.0472 AC: 1964 AN: 41570

American (AMR) AF: 0.178 AC: 2726 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3472

East Asian (EAS) AF: 0.0418 AC: 216 AN: 5168

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4828

European-Finnish (FIN) AF: 0.259 AC: 2735 AN: 10566

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18459 AN: 67980

Other (OTH) AF: 0.201 AC: 424 AN: 2108

Alfa AF: 0.238 Hom.: 13513

Bravo AF: 0.177

Asia WGS AF: 0.118 AC: 410 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	0.33
DANN	Benign	0.46
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12819853; hg19: chr12-91519856;