rs10129255

Positions:

• chr14-106767970-C-T

Variant summary

Our verdict is Likely benign. Variant got -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

Genes affected

IGH (HGNC:5477):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGH		n.106767970C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 7620 AN: 33622 Hom.: 472 Cov.: 5 FAILED QC

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

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.258

Alfa AF: 0.279 Hom.: 1658

Asia WGS AF: 0.402 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10129255; hg19: chr14-107176213;