16-77193699-TCG-ACA

Variant names:

• chr16-77193699-TCG-ACA
• NM_014940.4:c.397_399delTCGinsACA
• MON1B p.Ser133Thr

Variant summary

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

The NM_014940.4(MON1B):​c.397_399delTCGinsACA​(p.Ser133Thr) 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MON1B NM_014940.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.08
• Publications: 0 publications found

Genes affected

MON1B (HGNC:25020): (MON1 homolog B, secretory trafficking associated) Involved in early viral transcription and late viral transcription. Located in cytoplasm. Part of Mon1-Ccz1 complex. [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_014940.4. 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
	MON1B	NM_014940.4	MANE Select	c.397_399delTCGinsACA	p.Ser133Thr	missense	N/A	NP_055755.1	Q7L1V2-1
	MON1B	NM_001286639.2		c.149-636_149-634delTCGinsACA		intron	N/A	NP_001273568.1	E7EW32
	MON1B	NM_001286640.2		c.38-636_38-634delTCGinsACA		intron	N/A	NP_001273569.1	Q7L1V2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MON1B	ENST00000248248.8	TSL:1 MANE Select	c.397_399delTCGinsACA	p.Ser133Thr	missense	N/A	ENSP00000248248.3	Q7L1V2-1
	MON1B	ENST00000567291.5	TSL:3	c.397_399delTCGinsACA	p.Ser133Thr	missense	N/A	ENSP00000457858.1	H3BUX9
	MON1B	ENST00000569610.5	TSL:4	c.397_399delTCGinsACA	p.Ser133Thr	missense	N/A	ENSP00000456038.1	H3BR21

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		6.1

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: chr16-77227596;