8-80183160-C-T

Variant names:

• chr8-80183160-C-T
• rs998731
• ENST00000519250.5:n.235+35309G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519250.5(TPD52):​n.235+35309G>A variant causes a intron 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: TPD52 ENST00000519250.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 27 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]

LOC105375920 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519250.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPD52	ENST00000519250.5	TSL:4	n.235+35309G>A		intron	N/A
	TPD52	ENST00000520035.5	TSL:3	n.176-4881G>A		intron	N/A
	TPD52	ENST00000523564.2	TSL:5	n.63-22G>A		intron	N/A

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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.898 AC: 37281 AN: 41502

American (AMR) AF: 0.645 AC: 9856 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1755 AN: 3464

East Asian (EAS) AF: 0.786 AC: 4065 AN: 5170

South Asian (SAS) AF: 0.582 AC: 2797 AN: 4808

European-Finnish (FIN) AF: 0.482 AC: 5085 AN: 10540

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31188 AN: 67938

Other (OTH) AF: 0.593 AC: 1248 AN: 2106

Alfa AF: 0.527 Hom.: 55606

Bravo AF: 0.644

Asia WGS AF: 0.678 AC: 2359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.48
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs998731; hg19: chr8-81095395;