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GeneBe

rs998731

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The XR_929095.3(LOC105375920):n.593-22G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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

LOC105375920
XR_929095.3 intron, non_coding_transcript

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 -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105375920XR_929095.3 linkuse as main transcriptn.593-22G>C intron_variant, non_coding_transcript_variant
LOC105375920XR_929092.3 linkuse as main transcriptn.591-22G>C intron_variant, non_coding_transcript_variant
LOC105375920XR_929093.3 linkuse as main transcriptn.1182-22G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TPD52ENST00000519250.5 linkuse as main transcriptn.235+35309G>C intron_variant, non_coding_transcript_variant 4
TPD52ENST00000520035.5 linkuse as main transcriptn.176-4881G>C intron_variant, non_coding_transcript_variant 3
TPD52ENST00000523564.2 linkuse as main transcriptn.63-22G>C intron_variant, non_coding_transcript_variant 5
TPD52ENST00000602950.1 linkuse as main transcriptn.223-22G>C intron_variant, non_coding_transcript_variant 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