12-114656455-A-G

Variant names:

• chr12-114656455-A-G
• rs11067228

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.375 in 152,056 control chromosomes in the GnomAD database, including 12,050 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 0.38 (12050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 46 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57025 AN: 151938 Hom.: 12026 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.375 AC: 57078 AN: 152056 Hom.: 12050 Cov.: 32 AF XY: 0.379 AC XY: 28188 AN XY: 74328

African (AFR) AF: 0.168 AC: 6952 AN: 41470

American (AMR) AF: 0.512 AC: 7816 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2385 AN: 5156

South Asian (SAS) AF: 0.431 AC: 2078 AN: 4826

European-Finnish (FIN) AF: 0.389 AC: 4116 AN: 10574

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30514 AN: 67974

Other (OTH) AF: 0.412 AC: 868 AN: 2108

Alfa AF: 0.435 Hom.: 53985

Bravo AF: 0.378

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	17
DANN	Benign	0.86
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs11067228; hg19: chr12-115094260;