12-27097801-T-G

Variant names:

• chr12-27097801-T-G
• rs841245

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 0.226 in 152,148 control chromosomes in the GnomAD database, including 4,904 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 0.23 (4904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 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: 0.226 AC: 34343 AN: 152030 Hom.: 4905 Cov.: 32

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.226 AC: 34351 AN: 152148 Hom.: 4904 Cov.: 32 AF XY: 0.222 AC XY: 16495 AN XY: 74362

African (AFR) AF: 0.0864 AC: 3586 AN: 41502

American (AMR) AF: 0.170 AC: 2600 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3466

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5184

South Asian (SAS) AF: 0.165 AC: 797 AN: 4828

European-Finnish (FIN) AF: 0.315 AC: 3337 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22556 AN: 67980

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.174 Hom.: 438

Bravo AF: 0.207

Asia WGS AF: 0.0920 AC: 322 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	4.6
DANN	Benign	0.85
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs841245; hg19: chr12-27250734;