14-106539448-C-T

Variant names:

• chr14-106539448-C-T
• rs10151262

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 0.312 in 151,754 control chromosomes in the GnomAD database, including 8,600 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 0.31 (8600 hom., cov: 33)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 3 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 (Cadd=5.209).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47347 AN: 151644 Hom.: 8603 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.312 AC: 47350 AN: 151754 Hom.: 8600 Cov.: 33 AF XY: 0.310 AC XY: 22992 AN XY: 74178

African (AFR) AF: 0.120 AC: 4978 AN: 41414

American (AMR) AF: 0.407 AC: 6202 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2043 AN: 5086

South Asian (SAS) AF: 0.258 AC: 1232 AN: 4782

European-Finnish (FIN) AF: 0.368 AC: 3886 AN: 10560

Middle Eastern (MID) AF: 0.324 AC: 90 AN: 278

European-Non Finnish (NFE) AF: 0.393 AC: 26727 AN: 67926

Other (OTH) AF: 0.340 AC: 717 AN: 2106

Alfa AF: 0.334 Hom.: 1155

Bravo AF: 0.308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	5.2
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10151262;