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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGH		n.106772332C>T		intragenic_variant

Ensembl

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

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 v4.3

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;