7-30753937-AGC-TCA

Variant names:

• chr7-30753937-AGG-TCA
• NM_006774.5:c.361_362+1delAGGinsTCA
• INMT p.122

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP7

The NM_006774.5(INMT):​c.361_362+1delAGGinsTCA​(p.122) variant causes a splice donor, splice region, synonymous, intron 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. Synonymous variant affecting the same amino acid position (i.e. S121S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: INMT NM_006774.5 splice_donor, splice_region, synonymous, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.48
• Publications: 0 publications found

Genes affected

INMT (HGNC:6069): (indolethylamine N-methyltransferase) N-methylation of endogenous and xenobiotic compounds is a major method by which they are degraded. This gene encodes an enzyme that N-methylates indoles such as tryptamine. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream MINDY4 (aka FAM188B) gene. In rodents and other mammals such as cetartiodactyla this gene is in the opposite orientation compared to its orientation in human and other primates and this gene appears to have been lost in carnivora and chiroptera. [provided by RefSeq, Jul 2019]

INMT-MINDY4 (HGNC:41995): (INMT-MINDY4 readthrough (NMD candidate)) This locus represents rare but naturally occurring read-through transcription between the INMT (indolethylamine N-methyltransferase) and FAM188B (family with sequence similarity 188, member B) genes on chromosome 7. The read-through transcript is unlikely to produce a protein because it is a nonsense-mediated mRNA decay (NMD) candidate based on translation from the supported INMT start codon. [provided by RefSeq, Nov 2010]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP7: Synonymous conserved (PhyloP=3.48 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006774.5. 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
	INMT	NM_006774.5	MANE Select	c.361_362+1delAGGinsTCA	p.122	splice_donor splice_region synonymous intron	N/A	NP_006765.4
	INMT	NM_001199219.2		c.358_359+1delAGGinsTCA	p.121	splice_donor splice_region synonymous intron	N/A	NP_001186148.1	O95050-2
	INMT-MINDY4	NR_037598.1		n.374_375+1delAGGinsTCA		splice_donor splice_region intron non_coding_transcript_exon	Exon 2 of 20

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INMT	ENST00000013222.5	TSL:1 MANE Select	c.361_362+1delAGGinsTCA	p.122	splice_donor splice_region synonymous intron	N/A	ENSP00000013222.5	O95050-1
	INMT	ENST00000409539.1	TSL:1	c.358_359+1delAGGinsTCA	p.121	splice_donor splice_region synonymous intron	N/A	ENSP00000386961.1	O95050-2
	INMT-MINDY4	ENST00000458257.5	TSL:2	n.358_359+1delAGGinsTCA		splice_donor splice_region intron non_coding_transcript_exon	Exon 2 of 20	ENSP00000456039.1	F8WBC2

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		3.5

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: chr7-30793553;