6-30690903-CTC-TTG

Variant names:

• chr6-30690903-CTC-TTG
• NM_001384369.1:c.70_72delGAGinsCAA
• NRM p.Glu24Gln

Variant summary

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

The NM_001384369.1(NRM):​c.70_72delGAGinsCAA​(p.Glu24Gln) 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NRM NM_001384369.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.96
• Publications: 0 publications found

Genes affected

NRM (HGNC:8003): (nurim) The protein encoded by this gene contains transmembrane domains and resides within the inner nuclear membrane, where it is tightly associated with the nucleus. This protein shares homology with isoprenylcysteine carboxymethyltransferase enzymes. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384369.1. 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
	NRM	NM_001384369.1	MANE Select	c.70_72delGAGinsCAA	p.Glu24Gln	missense	N/A	NP_001371298.1	Q8IXM6-1
	NRM	NM_001270707.2		c.70_72delGAGinsCAA	p.Glu24Gln	missense	N/A	NP_001257636.1
	NRM	NM_007243.3		c.70_72delGAGinsCAA	p.Glu24Gln	missense	N/A	NP_009174.1	A0A1U9X845

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRM	ENST00000376421.7	TSL:1 MANE Select	c.70_72delGAGinsCAA	p.Glu24Gln	missense	N/A	ENSP00000365603.5	Q8IXM6-1
	NRM	ENST00000376420.9	TSL:1	c.70_72delGAGinsCAA	p.Glu24Gln	missense	N/A	ENSP00000365602.5	Q8IXM6-2
	NRM	ENST00000474864.5	TSL:1	n.70_72delGAGinsCAA		non_coding_transcript_exon	Exon 1 of 2

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		3.0

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: chr6-30658680;