rs717340

Positions:

• chr8-80134615-T-C

Variant summary

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

The NM_001025253.3(TPD52):​c.19+36810A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,060 control chromosomes in the GnomAD database, including 14,776 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 0.43 (14776 hom., cov: 32)
• Consequence: TPD52 NM_001025253.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.51

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPD52	NM_001025253.3	c.19+36810A>G		intron_variant		ENST00000518937.6
TPD52-MRPS28	NM_001387778.1	c.19+36810A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPD52	ENST00000518937.6	c.19+36810A>G		intron_variant		2	NM_001025253.3

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65606 AN: 151942 Hom.: 14778 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.455

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.432 AC: 65631 AN: 152060 Hom.: 14776 Cov.: 32 AF XY: 0.434 AC XY: 32299 AN XY: 74340

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.454

Alfa AF: 0.432 Hom.: 2288

Bravo AF: 0.435

Asia WGS AF: 0.579 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.077
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs717340; hg19: chr8-81046850;