NM_003288.4:c.311_312delGCinsTA

Variant names:

• chr20-63873813-GC-TA
• NM_003288.4:c.311_312delGCinsTA
• TPD52L2 p.Ser104Ile

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003288.4(TPD52L2):​c.311_312delGCinsTA​(p.Ser104Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S104N) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TPD52L2 NM_003288.4 missense, splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 0 publications found

Genes affected

TPD52L2 (HGNC:12007): (TPD52 like 2) This gene encodes a member of the tumor protein D52-like family. These proteins are characterized by an N-terminal coiled-coil motif that is used to form homo- and heteromeric complexes with other tumor protein D52-like proteins. Expression of this gene may be a marker for breast cancer and acute lymphoblastic leukemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 12. [provided by RefSeq, Aug 2011]

ENSG00000290226 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003288.4. 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
	TPD52L2	NM_003288.4	MANE Select	c.311_312delGCinsTA	p.Ser104Ile	missense splice_region	N/A	NP_003279.2
	TPD52L2	NM_199360.3		c.311_312delGCinsTA	p.Ser104Ile	missense splice_region	N/A	NP_955392.1	O43399-7
	TPD52L2	NM_001243895.2		c.311_312delGCinsTA	p.Ser104Ile	missense splice_region	N/A	NP_001230824.1	A0A087WYR3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPD52L2	ENST00000346249.9	TSL:1 MANE Select	c.311_312delGCinsTA	p.Ser104Ile	missense splice_region	N/A	ENSP00000343547.4	O43399-1
	TPD52L2	ENST00000352482.8	TSL:1	c.311_312delGCinsTA	p.Ser104Ile	missense splice_region	N/A	ENSP00000344647.4	O43399-5
	TPD52L2	ENST00000348257.9	TSL:1	c.311_312delGCinsTA	p.Ser104Ile	missense splice_region	N/A	ENSP00000343554.5	O43399-2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr20-62505166;