Genetic Variant DIS3L:p.Gly1030Glu (chr15-66333236-GA-AG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001143688.3(DIS3L):c.3089_3090delGAinsAG(p.Gly1030Glu) 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: 31)

Consequence

DIS3L
NM_001143688.3 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.65

Publications

0 publications found

Variant links:

Genes affected

DIS3L (HGNC:28698): (DIS3 like exosome 3'-5' exoribonuclease) The cytoplasmic RNA exosome complex degrades unstable mRNAs and is involved in the regular turnover of other mRNAs. The protein encoded by this gene contains 3'-5' exoribonuclease activity and is a catalytic component of this complex. [provided by RefSeq, May 2016]

DIS3L links:

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new If you want to explore the variant's impact on the transcript NM_001143688.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001143688.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DIS3L	NM_001143688.3	MANE Select	c.3089_3090delGAinsAG	p.Gly1030Glu	missense	N/A	NP_001137160.1	Q8TF46-1
DIS3L	NM_001323944.2		c.3038_3039delGAinsAG	p.Gly1013Glu	missense	N/A	NP_001310873.1
DIS3L	NM_001323948.2		c.2909_2910delGAinsAG	p.Gly970Glu	missense	N/A	NP_001310877.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DIS3L	ENST00000319212.9	TSL:5 MANE Select	c.3089_3090delGAinsAG	p.Gly1030Glu	missense	N/A	ENSP00000321711.4	Q8TF46-1
DIS3L	ENST00000319194.9	TSL:1	c.2840_2841delGAinsAG	p.Gly947Glu	missense	N/A	ENSP00000321583.5	Q8TF46-4
DIS3L	ENST00000530537.1	TSL:1	n.2599_2600delGAinsAG		non_coding_transcript_exon	Exon 16 of 16	ENSP00000432407.1	E9PKI7

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

6.7

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over