3-73062217-TCC-ACA

Variant names:

• chr3-73062217-TCC-ACA
• NM_018029.4:c.136_138delTCCinsACA
• EBLN2 p.Ser46Thr

Variant summary

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

The NM_018029.4(EBLN2):​c.136_138delTCCinsACA​(p.Ser46Thr) variant causes a missense 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.

• Frequency: Genomes: not found (cov: 31)
• Consequence: EBLN2 NM_018029.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 0 publications found

Genes affected

EBLN2 (HGNC:25493): (endogenous Bornavirus like nucleoprotein 2)

PPP4R2 (HGNC:18296): (protein phosphatase 4 regulatory subunit 2) The protein encoded by this gene is a regulatory subunit of the serine/threonine-protein phosphatase 4 complex. In addition to being required for efficient DNA double strand break repair, this complex plays a role in organization of microtubules at centrosomes and processing of spliceosomal snRNPs. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018029.4. 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
	EBLN2	NM_018029.4	MANE Select	c.136_138delTCCinsACA	p.Ser46Thr	missense	N/A	NP_060499.3	Q6P2I7
	PPP4R2	NM_174907.4	MANE Select	c.419+1157_419+1159delTCCinsACA		intron	N/A	NP_777567.1	Q9NY27-1
	PPP4R2	NM_001318026.2		c.305+1157_305+1159delTCCinsACA		intron	N/A	NP_001304955.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBLN2	ENST00000533473.1	TSL:6 MANE Select	c.136_138delTCCinsACA	p.Ser46Thr	missense	N/A	ENSP00000432104.1	Q6P2I7
	PPP4R2	ENST00000356692.10	TSL:1 MANE Select	c.419+1157_419+1159delTCCinsACA		intron	N/A	ENSP00000349124.5	Q9NY27-1
	PPP4R2	ENST00000710398.1		c.524+1157_524+1159delTCCinsACA		intron	N/A	ENSP00000518252.1	A0AA34QVI2

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		0.53

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: chr3-73111368;