rs7814569

chr8-80177631-A-G

Variant summary

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

The ENST00000519250.5(TPD52):n.235+40838T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,428 control chromosomes in the GnomAD database, including 6,517 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 0.22 (6517 hom., cov: 33)
  • Exomes 𝑓: 0.023 (0 hom.)
• Consequence: TPD52 ENST00000519250.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

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]

LOC105375920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375920	XR_929095.3			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPD52	ENST00000519250.5	n.235+40838T>C		intron_variant, non_coding_transcript_variant		4
TPD52	ENST00000523564.2			downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33294 AN: 152134 Hom.: 6502 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0811

Gnomad OTH AF: 0.196

GnomAD4 exome AF: 0.0227 AC: 4 AN: 176 Hom.: 0 Cov.: 0 AF XY: 0.0319 AC XY: 3 AN XY: 94

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0185

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.219 AC: 33359 AN: 152252 Hom.: 6517 Cov.: 33 AF XY: 0.219 AC XY: 16297 AN XY: 74440

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.0964

Gnomad4 NFE AF: 0.0811

Gnomad4 OTH AF: 0.194

Alfa AF: 0.120 Hom.: 1107

Bravo AF: 0.236

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.70
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7814569; hg19: chr8-81089866;