rs12884389

Variant names:

• chr14-105777786-C-A
• rs12884389

Your query was ambiguous. Multiple possible variants found:

• chr14-105777786-C-A
• chr14-105777786-C-G
• chr14-105777786-C-T

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 0.527 in 149,012 control chromosomes in the GnomAD database, including 22,819 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 0.53 (22819 hom., cov: 32)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 2 publications found

Genes affected

IGH (HGNC:5477):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.657 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: 0.527 AC: 78558 AN: 148932 Hom.: 22823 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.698

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.527 AC: 78560 AN: 149012 Hom.: 22819 Cov.: 32 AF XY: 0.517 AC XY: 37555 AN XY: 72608

African (AFR) AF: 0.353 AC: 14284 AN: 40440

American (AMR) AF: 0.430 AC: 6258 AN: 14560

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2682 AN: 3470

East Asian (EAS) AF: 0.0972 AC: 459 AN: 4724

South Asian (SAS) AF: 0.506 AC: 2263 AN: 4470

European-Finnish (FIN) AF: 0.561 AC: 5899 AN: 10510

Middle Eastern (MID) AF: 0.687 AC: 158 AN: 230

European-Non Finnish (NFE) AF: 0.662 AC: 44801 AN: 67638

Other (OTH) AF: 0.546 AC: 1125 AN: 2060

Alfa AF: 0.478 Hom.: 1537

Bravo AF: 0.504

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.63
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs12884389; hg19: chr14-106244123;