rs10129255

Variant names:

• chr14-106767970-C-T
• rs10129255

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.23 (465 hom., cov: 5)
  • Failed GnomAD Quality Control
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 17 publications found

Genes affected

IGH (HGNC:5477):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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: 0.227 AC: 7620 AN: 33622 Hom.: 472 Cov.: 5

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.261

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.226 AC: 7615 AN: 33632 Hom.: 465 Cov.: 5 AF XY: 0.225 AC XY: 3342 AN XY: 14862

African (AFR) AF: 0.301 AC: 2895 AN: 9618

American (AMR) AF: 0.210 AC: 620 AN: 2956

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 211 AN: 838

East Asian (EAS) AF: 0.281 AC: 374 AN: 1332

South Asian (SAS) AF: 0.448 AC: 378 AN: 844

European-Finnish (FIN) AF: 0.103 AC: 170 AN: 1652

Middle Eastern (MID) AF: 0.301 AC: 47 AN: 156

European-Non Finnish (NFE) AF: 0.178 AC: 2772 AN: 15588

Other (OTH) AF: 0.258 AC: 111 AN: 430

Alfa AF: 0.279 Hom.: 1658

Asia WGS AF: 0.402 AC: 1400 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	4.4
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10129255;

hg19: chr14-107176213;