rs34398108

Variant names:

• chr14-105702719-A-G
• rs34398108

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 0.477 in 151,568 control chromosomes in the GnomAD database, including 21,698 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 0.48 (21698 hom., cov: 34)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 4 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 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: 0.478 AC: 72347 AN: 151450 Hom.: 21701 Cov.: 34

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.477 AC: 72328 AN: 151568 Hom.: 21698 Cov.: 34 AF XY: 0.470 AC XY: 34778 AN XY: 74038

African (AFR) AF: 0.121 AC: 4997 AN: 41414

American (AMR) AF: 0.391 AC: 5937 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2400 AN: 3460

East Asian (EAS) AF: 0.492 AC: 2521 AN: 5128

South Asian (SAS) AF: 0.507 AC: 2420 AN: 4772

European-Finnish (FIN) AF: 0.594 AC: 6261 AN: 10548

Middle Eastern (MID) AF: 0.605 AC: 173 AN: 286

European-Non Finnish (NFE) AF: 0.677 AC: 45860 AN: 67764

Other (OTH) AF: 0.523 AC: 1096 AN: 2096

Alfa AF: 0.573 Hom.: 3529

Bravo AF: 0.445

Asia WGS AF: 0.491 AC: 1709 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.62
PhyloP100		-0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs34398108;

hg19: chr14-106169056;