NM_001025253.3:c.*1073C>T

Variant names:

• chr8-80037043-G-A
• rs10098470
• NM_001025253.3:c.*1073C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

ENSG00000276418 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025253.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPD52	NM_001025253.3	MANE Select	c.*1073C>T		3_prime_UTR	Exon 8 of 8	NP_001020424.1	P55327-4
	TPD52	NM_001287140.2		c.*1073C>T		3_prime_UTR	Exon 8 of 8	NP_001274069.1	P55327-6
	TPD52	NM_001287142.2		c.*1073C>T		3_prime_UTR	Exon 7 of 7	NP_001274071.1	P55327-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPD52	ENST00000518937.6	TSL:2 MANE Select	c.*1073C>T		3_prime_UTR	Exon 8 of 8	ENSP00000429915.1	P55327-4
	TPD52	ENST00000520527.5	TSL:1	c.*1073C>T		3_prime_UTR	Exon 8 of 8	ENSP00000429309.1	P55327-6
	TPD52	ENST00000448733.3	TSL:1	c.*1073C>T		3_prime_UTR	Exon 7 of 7	ENSP00000410222.2	P55327-5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0211 AC: 9 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.397 AC: 16468 AN: 41434

American (AMR) AF: 0.0768 AC: 1175 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3468

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5186

South Asian (SAS) AF: 0.0300 AC: 145 AN: 4826

European-Finnish (FIN) AF: 0.0237 AC: 251 AN: 10582

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0300 AC: 2041 AN: 67976

Other (OTH) AF: 0.128 AC: 271 AN: 2112

Alfa AF: 0.0590 Hom.: 995

Bravo AF: 0.150

Asia WGS AF: 0.0570 AC: 197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10098470; hg19: chr8-80949278;