12-114247766-A-G

Variant names:

• chr12-114247766-A-G
• rs1270884

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 0.625 in 152,090 control chromosomes in the GnomAD database, including 30,938 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 0.62 (30938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 54 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94895 AN: 151972 Hom.: 30879 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.625 AC: 95011 AN: 152090 Hom.: 30938 Cov.: 32 AF XY: 0.626 AC XY: 46521 AN XY: 74316

African (AFR) AF: 0.805 AC: 33405 AN: 41504

American (AMR) AF: 0.656 AC: 10028 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1805 AN: 3468

East Asian (EAS) AF: 0.744 AC: 3850 AN: 5172

South Asian (SAS) AF: 0.611 AC: 2943 AN: 4818

European-Finnish (FIN) AF: 0.560 AC: 5906 AN: 10544

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34962 AN: 67982

Other (OTH) AF: 0.613 AC: 1298 AN: 2116

Alfa AF: 0.554 Hom.: 42041

Bravo AF: 0.641

Asia WGS AF: 0.701 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.69
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1270884; hg19: chr12-114685571;