6-152721838-GA-AG

Variant names:

• chr6-152721838-GA-AG
• NM_025107.3:c.293_294delGAinsAG
• MYCT1 p.Arg98Lys

Variant summary

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

The NM_025107.3(MYCT1):​c.293_294delGAinsAG​(p.Arg98Lys) 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R98T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYCT1 NM_025107.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.56
• Publications: 0 publications found

Genes affected

MYCT1 (HGNC:23172): (MYC target 1) Predicted to act upstream of or within hematopoietic stem cell homeostasis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025107.3. 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
	MYCT1	NM_025107.3	MANE Select	c.293_294delGAinsAG	p.Arg98Lys	missense	N/A	NP_079383.2	Q8N699
	MYCT1	NM_001371624.1		c.149_150delGAinsAG	p.Arg50Lys	missense	N/A	NP_001358553.1	D6Q1S4
	MYCT1	NM_001371625.1		c.149_150delGAinsAG	p.Arg50Lys	missense	N/A	NP_001358554.1	D6Q1S4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYCT1	ENST00000367245.6	TSL:1 MANE Select	c.293_294delGAinsAG	p.Arg98Lys	missense	N/A	ENSP00000356214.5	Q8N699
	MYCT1	ENST00000532295.1	TSL:3	c.233_234delGAinsAG	p.Arg78Lys	missense	N/A	ENSP00000434396.1	H0YDV5
	MYCT1	ENST00000529453.1	TSL:3	c.197-925_197-924delGAinsAG		intron	N/A	ENSP00000432612.1	E9PQ55

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		5.6

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: chr6-153042973;