10-15796155-GG-TA

Variant names:

• chr10-15796155-GG-TA
• NM_024948.4:c.899_900delCCinsTA
• MINDY3 p.Ala300Val

Variant summary

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

The NM_024948.4(MINDY3):​c.899_900delCCinsTA​(p.Ala300Val) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A300T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MINDY3 NM_024948.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.46
• Publications: 0 publications found

Genes affected

MINDY3 (HGNC:23578): (MINDY lysine 48 deubiquitinase 3) The protein encoded by this gene contains a caspase-associated recruitment domain and may function in apoptosis. It has been identified as a tumor suppressor in lung and gastric cancers, and a polymorphism in the gene may be associated with gastric cancer risk. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ENSG00000293819 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024948.4. 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
	MINDY3	NM_024948.4	MANE Select	c.899_900delCCinsTA	p.Ala300Val	missense	N/A	NP_079224.1	Q9H8M7-1
	MINDY3	NM_001318330.2		c.380_381delCCinsTA	p.Ala127Val	missense	N/A	NP_001305259.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MINDY3	ENST00000277632.8	TSL:1 MANE Select	c.899_900delCCinsTA	p.Ala300Val	missense	N/A	ENSP00000277632.3	Q9H8M7-1
	MINDY3	ENST00000477891.1	TSL:1	n.1046_1047delCCinsTA		non_coding_transcript_exon	Exon 10 of 14
	MINDY3	ENST00000953409.1		c.899_900delCCinsTA	p.Ala300Val	missense	N/A	ENSP00000623468.1

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		6.5

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: chr10-15838154;