NME9 p.Glu151Glu

Variant names:

• chr3-138314338-C-C
• NM_001349018.2:c.

Your query was ambiguous. Multiple possible variants found:

• chr3-138314339--
• chr3-138314339-C-T

Variant summary

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

The NM_001349018.2(NME9):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NME9 NM_001349018.2 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 0 publications found

Genes affected

NME9 (HGNC:21343): (NME/NM23 family member 9) Predicted to enable nucleoside diphosphate kinase activity. Predicted to be involved in nucleotide metabolic process. Predicted to be located in dynein axonemal particle. [provided by Alliance of Genome Resources, Apr 2022]

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_001349018.2. 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
	NME9	NM_001349018.2	MANE Select	c.		exon_region	Exon 6 of 11	NP_001335947.1	Q86XW9-1
	NME9	NM_001349024.2		c.		exon_region	Exon 6 of 11	NP_001335953.1
	NME9	NM_001349025.2		c.		exon_region	Exon 5 of 10	NP_001335954.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NME9	ENST00000333911.9	TSL:1 MANE Select	c.		exon_region	Exon 6 of 11	ENSP00000335444.3	Q86XW9-1
	NME9	ENST00000492993.5	TSL:1	n.		exon_region	Exon 4 of 8	ENSP00000419355.1	Q3KNW3
	NME9	ENST00000953094.1		c.		exon_region	Exon 8 of 13	ENSP00000623153.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.36

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: chr3-138033180;