chr2-232053189-C-T

Position:

• chr2-232053189-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152383.5(DIS3L2):​c.366+23109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,220 control chromosomes in the GnomAD database, including 25,537 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (25537 hom., cov: 33)
• Consequence: DIS3L2 NM_152383.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIS3L2	NM_152383.5	c.366+23109C>T		intron_variant		ENST00000325385.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIS3L2	ENST00000325385.12	c.366+23109C>T		intron_variant		5	NM_152383.5	P1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85733 AN: 152102 Hom.: 25528 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.563 AC: 85766 AN: 152220 Hom.: 25537 Cov.: 33 AF XY: 0.570 AC XY: 42426 AN XY: 74428

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.538

Alfa AF: 0.604 Hom.: 11883

Bravo AF: 0.546

Asia WGS AF: 0.455 AC: 1584 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.7
DANN	Benign	0.64

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: rs1453867; hg19: chr2-232917899;