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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGH		n.106779223C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;