rs10098470

chr8-80037043-G-Achr8-80037043-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001025253.3(TPD52):c.*1073C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,516 control chromosomes in the GnomAD database, including 3,424 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 0.13 (3423 hom., cov: 32)
  • Exomes 𝑓: 0.021 (1 hom.)
• Consequence: TPD52 NM_001025253.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

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]

TPD52-MRPS28 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPD52	NM_001025253.3	c.*1073C>T		3_prime_UTR_variant	8/8	ENST00000518937.6
TPD52-MRPS28	NM_001387778.1	c.435+5577C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPD52	ENST00000518937.6	c.*1073C>T		3_prime_UTR_variant	8/8	2	NM_001025253.3

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20475 AN: 151966 Hom.: 3417 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.0237

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.0208 AC: 9 AN: 432 Hom.: 1 Cov.: 0 AF XY: 0.0192 AC XY: 5 AN XY: 260

Gnomad4 FIN exome AF: 0.0211

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.135 AC: 20509 AN: 152084 Hom.: 3423 Cov.: 32 AF XY: 0.131 AC XY: 9717 AN XY: 74364

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.0300

Gnomad4 FIN AF: 0.0237

Gnomad4 NFE AF: 0.0300

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0531 Hom.: 648

Bravo AF: 0.150

Asia WGS AF: 0.0570 AC: 197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.2
Dann	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10098470; hg19: chr8-80949278;