chr14-106775945-T-A

Variant names:

• chr14-106775945-T-A
• rs10150241

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 0.318 in 152,144 control chromosomes in the GnomAD database, including 8,242 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 0.32 (8242 hom., cov: 33)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• 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 (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

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: 0.318 AC: 48312 AN: 152026 Hom.: 8217 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.318 AC: 48391 AN: 152144 Hom.: 8242 Cov.: 33 AF XY: 0.321 AC XY: 23864 AN XY: 74364

African (AFR) AF: 0.411 AC: 17035 AN: 41474

American (AMR) AF: 0.275 AC: 4210 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1279 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1799 AN: 5174

South Asian (SAS) AF: 0.495 AC: 2387 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2887 AN: 10580

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17828 AN: 68004

Other (OTH) AF: 0.307 AC: 649 AN: 2116

Alfa AF: 0.288 Hom.: 853

Bravo AF: 0.320

Asia WGS AF: 0.412 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.51
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10150241; hg19: chr14-107184184; COSMIC: COSV66753587;