14-106772332-C-T

Variant names:

• chr14-106772332-C-T
• rs2337406

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00565 in 140,464 control chromosomes in the GnomAD database, including 6 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 0.0057 (6 hom., cov: 27)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 8 publications found

Genes affected

IGH (HGNC:5477):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS2: High Homozygotes in GnomAd4 at 6 gene

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: 0.00566 AC: 794 AN: 140350 Hom.: 6 Cov.: 27

Gnomad AFR AF: 0.00647

Gnomad AMI AF: 0.00235

Gnomad AMR AF: 0.00482

Gnomad ASJ AF: 0.00694

Gnomad EAS AF: 0.00516

Gnomad SAS AF: 0.00677

Gnomad FIN AF: 0.00563

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00515

Gnomad OTH AF: 0.0117

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

GnomAD4 genome AF: 0.00565 AC: 794 AN: 140464 Hom.: 6 Cov.: 27 AF XY: 0.00665 AC XY: 455 AN XY: 68456

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00645 AC: 243 AN: 37694

American (AMR) AF: 0.00482 AC: 67 AN: 13914

Ashkenazi Jewish (ASJ) AF: 0.00694 AC: 22 AN: 3172

East Asian (EAS) AF: 0.00517 AC: 25 AN: 4832

South Asian (SAS) AF: 0.00677 AC: 30 AN: 4434

European-Finnish (FIN) AF: 0.00563 AC: 56 AN: 9942

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.00515 AC: 327 AN: 63452

Other (OTH) AF: 0.0116 AC: 22 AN: 1896

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0308 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.59
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2337406; hg19: chr14-107180574;