12-88645023-C-T

Variant names:

• chr12-88645023-C-T
• rs1881227

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 0.746 in 152,052 control chromosomes in the GnomAD database, including 48,973 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 0.75 (48973 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 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: 0.747 AC: 113481 AN: 151932 Hom.: 48966 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.746 AC: 113493 AN: 152052 Hom.: 48973 Cov.: 31 AF XY: 0.753 AC XY: 55957 AN XY: 74338

African (AFR) AF: 0.275 AC: 11388 AN: 41402

American (AMR) AF: 0.868 AC: 13248 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 3221 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3862 AN: 5154

South Asian (SAS) AF: 0.891 AC: 4296 AN: 4822

European-Finnish (FIN) AF: 0.957 AC: 10145 AN: 10606

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64433 AN: 68010

Other (OTH) AF: 0.824 AC: 1741 AN: 2114

Alfa AF: 0.912 Hom.: 50285

Bravo AF: 0.717

Asia WGS AF: 0.771 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.20
DANN	Benign	0.77
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1881227; hg19: chr12-89038800;