19-55080238-CG-AA

Variant names:

• chr19-55080238-CG-AA
• NM_133180.3:c.389_390delCGinsAA
• EPS8L1 p.Ala130Glu

Variant summary

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

The NM_133180.3(EPS8L1):​c.389_390delCGinsAA​(p.Ala130Glu) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A130P) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: EPS8L1 NM_133180.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 0 publications found

Genes affected

EPS8L1 (HGNC:21295): (EPS8 signaling adaptor L1) This gene encodes a protein that is related to epidermal growth factor receptor pathway substrate 8 (EPS8), a substrate for the epidermal growth factor receptor. The function of this protein is unknown. At least two alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133180.3. 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
	EPS8L1	NM_133180.3	MANE Select	c.389_390delCGinsAA	p.Ala130Glu	missense	N/A	NP_573441.2	Q8TE68-1
	EPS8L1	NM_017729.4		c.-256_-255delCGinsAA		upstream_gene	N/A	NP_060199.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPS8L1	ENST00000201647.11	TSL:1 MANE Select	c.389_390delCGinsAA	p.Ala130Glu	missense	N/A	ENSP00000201647.5	Q8TE68-1
	EPS8L1	ENST00000587786.5	TSL:1	n.275_276delCGinsAA		non_coding_transcript_exon	Exon 4 of 14	ENSP00000465830.1	K7EKX9
	EPS8L1	ENST00000592824.5	TSL:1	n.493_494delCGinsAA		non_coding_transcript_exon	Exon 6 of 15

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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.10

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: chr19-55591606;