chr14-106771605-C-T

Variant names:

• chr14-106771605-C-T
• rs2007467

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 0.264 in 140,818 control chromosomes in the GnomAD database, including 6,199 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 0.26 (6199 hom., cov: 23)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGH		n.106771605C>T		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.265 AC: 37223 AN: 140694 Hom.: 6201 Cov.: 23

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.264 AC: 37242 AN: 140818 Hom.: 6199 Cov.: 23 AF XY: 0.268 AC XY: 18387 AN XY: 68500

African (AFR) AF: 0.210 AC: 7978 AN: 37986

American (AMR) AF: 0.266 AC: 3704 AN: 13942

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 954 AN: 3170

East Asian (EAS) AF: 0.370 AC: 1697 AN: 4592

South Asian (SAS) AF: 0.487 AC: 2002 AN: 4110

European-Finnish (FIN) AF: 0.283 AC: 2810 AN: 9946

Middle Eastern (MID) AF: 0.344 AC: 93 AN: 270

European-Non Finnish (NFE) AF: 0.270 AC: 17297 AN: 64072

Other (OTH) AF: 0.273 AC: 512 AN: 1878

Alfa AF: 0.214 Hom.: 1335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.3
DANN	Benign	0.57
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2007467; hg19: chr14-107179847;