8-80119587-A-G

Variant summary

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

The NM_001025253.3(TPD52):c.19+51838T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,084 control chromosomes in the GnomAD database, including 33,444 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 0.65 (33444 hom., cov: 32)
• Consequence: TPD52 NM_001025253.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPD52	NM_001025253.3	c.19+51838T>C		intron_variant		ENST00000518937.6
TPD52-MRPS28	NM_001387778.1	c.19+51838T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPD52	ENST00000518937.6	c.19+51838T>C		intron_variant		2	NM_001025253.3

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98327 AN: 151966 Hom.: 33402 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.647 AC: 98428 AN: 152084 Hom.: 33444 Cov.: 32 AF XY: 0.646 AC XY: 48062 AN XY: 74350

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.653

Alfa AF: 0.584 Hom.: 3162

Bravo AF: 0.666

Asia WGS AF: 0.711 AC: 2468 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10957961; hg19: chr8-81031822;