6-82365309-GCTGGCGGAGCTGGCCGCGCTCAAC-G

Variant names:

• chr6-82365309-GCTGGCGGAGCTGGCCGCGCTCAAC-G
• NM_001376922.1:c.351_374delGGCGGAGCTGGCCGCGCTCAACCT

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PM4

The NM_001376922.1(TPBG):​c.351_374delGGCGGAGCTGGCCGCGCTCAACCT​(p.Ala118_Leu125del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: TPBG NM_001376922.1 disruptive_inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.07

Genes affected

TPBG (HGNC:12004): (trophoblast glycoprotein) This gene encodes a leucine-rich transmembrane glycoprotein that may be involved in cell adhesion. The encoded protein is an oncofetal antigen that is specific to trophoblast cells. In adults this protein is highly expressed in many tumor cells and is associated with poor clinical outcome in numerous cancers. Alternate splicing in the 5' UTR results in multiple transcript variants that encode the same protein. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_001376922.1.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPBG	NM_001376922.1	c.351_374delGGCGGAGCTGGCCGCGCTCAACCT	p.Ala118_Leu125del	disruptive_inframe_deletion	Exon 2 of 2	ENST00000369750.4	NP_001363851.1
TPBG	NM_001166392.2	c.351_374delGGCGGAGCTGGCCGCGCTCAACCT	p.Ala118_Leu125del	disruptive_inframe_deletion	Exon 2 of 2		NP_001159864.1
TPBG	NM_006670.5	c.351_374delGGCGGAGCTGGCCGCGCTCAACCT	p.Ala118_Leu125del	disruptive_inframe_deletion	Exon 3 of 3		NP_006661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPBG	ENST00000369750.4	c.351_374delGGCGGAGCTGGCCGCGCTCAACCT	p.Ala118_Leu125del	disruptive_inframe_deletion	Exon 2 of 2	1	NM_001376922.1	ENSP00000358765.4
TPBG	ENST00000535040.4	c.351_374delGGCGGAGCTGGCCGCGCTCAACCT	p.Ala118_Leu125del	disruptive_inframe_deletion	Exon 3 of 3	2		ENSP00000441219.1
TPBG	ENST00000543496.3	c.351_374delGGCGGAGCTGGCCGCGCTCAACCT	p.Ala118_Leu125del	disruptive_inframe_deletion	Exon 2 of 2	2		ENSP00000440049.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Apr 16, 2021

New York Genome Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-83075026;