14-106771605-C-T

Variant names:

• chr14-106771605-C-T
• rs2007467

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 0.264 in 140,818 control chromosomes in the GnomAD database, including 6,199 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 0.26 (6199 hom., cov: 23)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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: 0.265 AC: 37223 AN: 140694 Hom.: 6201 Cov.: 23

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.264 AC: 37242 AN: 140818 Hom.: 6199 Cov.: 23 AF XY: 0.268 AC XY: 18387 AN XY: 68500

African (AFR) AF: 0.210 AC: 7978 AN: 37986

American (AMR) AF: 0.266 AC: 3704 AN: 13942

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 954 AN: 3170

East Asian (EAS) AF: 0.370 AC: 1697 AN: 4592

South Asian (SAS) AF: 0.487 AC: 2002 AN: 4110

European-Finnish (FIN) AF: 0.283 AC: 2810 AN: 9946

Middle Eastern (MID) AF: 0.344 AC: 93 AN: 270

European-Non Finnish (NFE) AF: 0.270 AC: 17297 AN: 64072

Other (OTH) AF: 0.273 AC: 512 AN: 1878

Alfa AF: 0.214 Hom.: 1335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.3
DANN	Benign	0.57
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2007467; hg19: chr14-107179847;