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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGH		n.105702719A>G		intragenic_variant

Ensembl

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

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 v4.3

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

Other links and lift over

dbSNP: rs34398108; hg19: chr14-106169056;