rs12590667

Variant names:

• chr14-106779223-C-T
• rs12590667

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 0.318 in 151,980 control chromosomes in the GnomAD database, including 8,288 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 0.32 (8288 hom., cov: 33)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 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: 0.318 AC: 48303 AN: 151862 Hom.: 8263 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.318 AC: 48381 AN: 151980 Hom.: 8288 Cov.: 33 AF XY: 0.321 AC XY: 23868 AN XY: 74296

African (AFR) AF: 0.412 AC: 17047 AN: 41418

American (AMR) AF: 0.276 AC: 4216 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1793 AN: 5168

South Asian (SAS) AF: 0.494 AC: 2380 AN: 4814

European-Finnish (FIN) AF: 0.273 AC: 2890 AN: 10568

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.262 AC: 17810 AN: 67940

Other (OTH) AF: 0.309 AC: 651 AN: 2108

Alfa AF: 0.293 Hom.: 1140

Bravo AF: 0.320

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.0
DANN	Benign	0.22
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12590667; hg19: chr14-107187462;