NM_006887.5:c.1426dupA

Variant names:

• chr2-43224377-C-CT
• rs1558427702
• NM_006887.5:c.1426dupA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_006887.5(ZFP36L2):​c.1426dupA​(p.Ser476LysfsTer55) variant causes a frameshift 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 not provided (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZFP36L2 NM_006887.5 frameshift
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 1.64
• Publications: 0 publications found

Genes affected

ZFP36L2 (HGNC:1108): (ZFP36 ring finger protein like 2) This gene is a member of the TIS11 family of early response genes. Family members are induced by various agonists such as the phorbol ester TPA and the polypeptide mitogen EGF. The encoded protein contains a distinguishing putative zinc finger domain with a repeating cys-his motif. This putative nuclear transcription factor most likely functions in regulating the response to growth factors. [provided by RefSeq, Jul 2008]

LINC01126 (HGNC:49275): (long intergenic non-protein coding RNA 1126)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006887.5. 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
	ZFP36L2	NM_006887.5	MANE Select	c.1426dupA	p.Ser476LysfsTer55	frameshift	Exon 2 of 2	NP_008818.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP36L2	ENST00000282388.4	TSL:1 MANE Select	c.1426dupA	p.Ser476LysfsTer55	frameshift	Exon 2 of 2	ENSP00000282388.3	P47974
	ZFP36L2	ENST00000929034.1		c.1420dupA	p.Ser474LysfsTer55	frameshift	Exon 2 of 2	ENSP00000599093.1
	ZFP36L2	ENST00000929033.1		c.1408dupA	p.Ser470LysfsTer55	frameshift	Exon 2 of 2	ENSP00000599092.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6
Mutation Taster		=2/198	disease causing

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: rs1558427702; hg19: chr2-43451516;