rs372560799

Positions:

• chr2-232334452-C-A
• chr2-232334452-C-G
• chr2-232334452-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_152383.5(DIS3L2):​c.2242C>A​(p.Arg748Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. 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. R748C) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DIS3L2 NM_152383.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00

Genes affected

DIS3L2 (HGNC:28648): (DIS3 like 3'-5' exoribonuclease 2) The protein encoded by this gene is similar in sequence to 3'/5' exonucleolytic subunits of the RNA exosome. The exosome is a large multimeric ribonucleotide complex responsible for degrading various RNA substrates. Several transcript variants, some protein-coding and some not, have been found for this gene. [provided by RefSeq, Mar 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19493833).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIS3L2	NM_152383.5	c.2242C>A	p.Arg748Ser	missense_variant	18/21	ENST00000325385.12
DIS3L2	NM_001257281.2	c.1582-8893C>A		intron_variant
DIS3L2	NR_046476.2	n.2315C>A		non_coding_transcript_exon_variant	18/21
DIS3L2	NR_046477.2	n.2294C>A		non_coding_transcript_exon_variant	17/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIS3L2	ENST00000325385.12	c.2242C>A	p.Arg748Ser	missense_variant	18/21	5	NM_152383.5	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.67
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Uncertain	25
DANN	Benign	0.97
DEOGEN2	Benign	0.017	T;T;T
Eigen	Benign	-0.032
Eigen_PC	Benign	-0.059
FATHMM_MKL	Benign	0.70	D
LIST_S2	Uncertain	0.92	D;.;D
M_CAP	Benign	0.073	D
MetaRNN	Benign	0.14	T;T;T
MetaSVM	Benign	-0.85	T
MutationAssessor	Benign	2.0	M;M;.
MutationTaster	Benign	0.90	D;D;D
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-2.1	N;N;N
REVEL	Benign	0.081
Sift	Benign	0.050	D;D;D
Sift4G	Benign	0.32	T;T;D
Polyphen		0.18	B;B;.
Vest4		0.78
MutPred		0.45		Loss of MoRF binding (P = 0.0409);Loss of MoRF binding (P = 0.0409);.;
MVP		0.043
MPC		0.48
ClinPred		0.81	D
GERP RS		2.9
Varity_R		0.27
gMVP		0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs372560799; hg19: chr2-233199162;