14-105782836-C-G

Variant names:

• chr14-105782836-C-G
• rs2725142

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 0.305 in 149,264 control chromosomes in the GnomAD database, including 8,629 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 0.30 (8629 hom., cov: 31)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 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: 0.305 AC: 45467 AN: 149178 Hom.: 8612 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.305 AC: 45502 AN: 149264 Hom.: 8629 Cov.: 31 AF XY: 0.319 AC XY: 23238 AN XY: 72766

African (AFR) AF: 0.109 AC: 4414 AN: 40606

American (AMR) AF: 0.510 AC: 7448 AN: 14602

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2274 AN: 4684

South Asian (SAS) AF: 0.465 AC: 2097 AN: 4506

European-Finnish (FIN) AF: 0.443 AC: 4675 AN: 10548

Middle Eastern (MID) AF: 0.272 AC: 62 AN: 228

European-Non Finnish (NFE) AF: 0.337 AC: 22780 AN: 67670

Other (OTH) AF: 0.316 AC: 645 AN: 2040

Alfa AF: 0.310 Hom.: 1030

Bravo AF: 0.304

Asia WGS AF: 0.434 AC: 1488 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.5
DANN	Benign	0.80
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2725142; hg19: chr14-106249173;