chr14-106582055-G-C

Variant names:

• chr14-106582055-G-C
• rs8011590

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 0.0997 in 151,944 control chromosomes in the GnomAD database, including 886 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 0.10 (886 hom., cov: 32)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 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: 0.0997 AC: 15136 AN: 151828 Hom.: 886 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0274

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0677

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.0997 AC: 15145 AN: 151944 Hom.: 886 Cov.: 32 AF XY: 0.103 AC XY: 7628 AN XY: 74258

African (AFR) AF: 0.133 AC: 5529 AN: 41420

American (AMR) AF: 0.134 AC: 2038 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.157 AC: 796 AN: 5082

South Asian (SAS) AF: 0.237 AC: 1141 AN: 4812

European-Finnish (FIN) AF: 0.0274 AC: 290 AN: 10594

Middle Eastern (MID) AF: 0.108 AC: 31 AN: 286

European-Non Finnish (NFE) AF: 0.0678 AC: 4608 AN: 68004

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.0292 Hom.: 17

Bravo AF: 0.107

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.023
DANN	Benign	0.39
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs8011590; hg19: chr14-107038041;