2-232290856-T-C

Variant names:

• chr2-232290856-T-C
• rs6718438
• NM_152383.5:c.1660-9184T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_152383.5(DIS3L2):​c.1660-9184T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,072 control chromosomes in the GnomAD database, including 9,662 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 0.33 (9662 hom., cov: 32)
• Consequence: DIS3L2 NM_152383.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIS3L2	NM_152383.5	c.1660-9184T>C		intron_variant	Intron 13 of 20	ENST00000325385.12	NP_689596.4
DIS3L2	NM_001257281.2	c.1581+27494T>C		intron_variant	Intron 13 of 13		NP_001244210.1
DIS3L2	NR_046476.2	n.1806-9184T>C		intron_variant	Intron 13 of 20
DIS3L2	NR_046477.2	n.1782-9184T>C		intron_variant	Intron 12 of 18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIS3L2	ENST00000325385.12	c.1660-9184T>C		intron_variant	Intron 13 of 20	5	NM_152383.5	ENSP00000315569.7

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49630 AN: 151954 Hom.: 9634 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.327 AC: 49715 AN: 152072 Hom.: 9662 Cov.: 32 AF XY: 0.326 AC XY: 24234 AN XY: 74350

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.329

Alfa AF: 0.254 Hom.: 2989

Bravo AF: 0.357

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	21
DANN	Benign	0.71

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: rs6718438; hg19: chr2-233155566;