8-80183160-C-T

Variant summary

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

The XR_929095.3(LOC105375920):n.593-22G>A 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 0.617 in 152,018 control chromosomes in the GnomAD database, including 31,739 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 0.62 (31738 hom., cov: 31)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: LOC105375920 XR_929095.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

Genes affected

LOC105375920 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375920	XR_929095.3	n.593-22G>A		intron_variant, non_coding_transcript_variant
LOC105375920	XR_929092.3	n.591-22G>A		intron_variant, non_coding_transcript_variant
LOC105375920	XR_929093.3	n.1182-22G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPD52	ENST00000519250.5	n.235+35309G>A		intron_variant, non_coding_transcript_variant		4
TPD52	ENST00000520035.5	n.176-4881G>A		intron_variant, non_coding_transcript_variant		3
TPD52	ENST00000523564.2	n.63-22G>A		intron_variant, non_coding_transcript_variant		5
TPD52	ENST00000602950.1	n.223-22G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93653 AN: 151894 Hom.: 31672 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.594

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.617 AC: 93778 AN: 152012 Hom.: 31738 Cov.: 31 AF XY: 0.619 AC XY: 45958 AN XY: 74278

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.593

Alfa AF: 0.517 Hom.: 13874

Bravo AF: 0.644

Asia WGS AF: 0.678 AC: 2359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs998731; hg19: chr8-81095395;