NM_007036.5:c.472_474delGATinsTAC

Variant names:

• chr5-54979413-ATC-GTA
• NM_007036.5:c.472_474delGATinsTAC
• ESM1 p.Asp158Tyr

Variant summary

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

The NM_007036.5(ESM1):​c.472_474delGATinsTAC​(p.Asp158Tyr) variant causes a missense change. 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. D158N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ESM1 NM_007036.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.50
• Publications: 0 publications found

Genes affected

ESM1 (HGNC:3466): (endothelial cell specific molecule 1) This gene encodes a secreted protein which is mainly expressed in the endothelial cells in human lung and kidney tissues. The expression of this gene is regulated by cytokines, suggesting that it may play a role in endothelium-dependent pathological disorders. The transcript contains multiple polyadenylation and mRNA instability signals. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007036.5. 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
	ESM1	NM_007036.5	MANE Select	c.472_474delGATinsTAC	p.Asp158Tyr	missense	N/A	NP_008967.1	Q9NQ30-1
	ESM1	NM_001135604.2		c.322_324delGATinsTAC	p.Asp108Tyr	missense	N/A	NP_001129076.1	Q9NQ30-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ESM1	ENST00000381405.5	TSL:1 MANE Select	c.472_474delGATinsTAC	p.Asp158Tyr	missense	N/A	ENSP00000370812.4	Q9NQ30-1
	ESM1	ENST00000381403.4	TSL:1	c.322_324delGATinsTAC	p.Asp108Tyr	missense	N/A	ENSP00000370810.4	Q9NQ30-2
	ESM1	ENST00000598310.5	TSL:5	n.250_252delGATinsTAC		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.5

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: chr5-54275241;