rs1042638

Variant names:

• chr8-80037711-G-A
• rs1042638
• NM_001025253.3:c.*405C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-80037711-G-A
• chr8-80037711-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001025253.3(TPD52):​c.*405C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TPD52 NM_001025253.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 4 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]

ENSG00000276418 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025253.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPD52	NM_001025253.3	MANE Select	c.*405C>T		3_prime_UTR	Exon 8 of 8	NP_001020424.1	P55327-4
	TPD52	NM_001287140.2		c.*405C>T		3_prime_UTR	Exon 8 of 8	NP_001274069.1	P55327-6
	TPD52	NM_001287142.2		c.*405C>T		3_prime_UTR	Exon 7 of 7	NP_001274071.1	P55327-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPD52	ENST00000518937.6	TSL:2 MANE Select	c.*405C>T		3_prime_UTR	Exon 8 of 8	ENSP00000429915.1	P55327-4
	TPD52	ENST00000520527.5	TSL:1	c.*405C>T		3_prime_UTR	Exon 8 of 8	ENSP00000429309.1	P55327-6
	TPD52	ENST00000448733.3	TSL:1	c.*405C>T		3_prime_UTR	Exon 7 of 7	ENSP00000410222.2	P55327-5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000142 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.8
DANN	Benign	0.66
PhyloP100		-0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1042638; hg19: chr8-80949946;