GeneBe

rs998731

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000520035.5(TPD52):​n.176-4881G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

TPD52
ENST00000520035.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0690
Variant links:
Genes affected
TPD52 (HGNC:12005): (tumor protein D52) Enables calcium ion binding activity and protein homodimerization activity. Involved in B cell differentiation. Located in endoplasmic reticulum and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105375920XR_929092.3 linkn.591-22G>C intron_variant Intron 2 of 3
LOC105375920XR_929093.3 linkn.1182-22G>C intron_variant Intron 2 of 3
LOC105375920XR_929095.3 linkn.593-22G>C intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TPD52ENST00000519250.5 linkn.235+35309G>C intron_variant Intron 2 of 4 4
TPD52ENST00000520035.5 linkn.176-4881G>C intron_variant Intron 2 of 2 3
TPD52ENST00000523564.2 linkn.63-22G>C intron_variant Intron 1 of 2 5
TPD52ENST00000602950.1 linkn.223-22G>C intron_variant Intron 2 of 2 5

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.71
DANN
Benign
0.29

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs998731; hg19: chr8-81095395; API