rs790040

Positions:

• chr2-232444838-G-A
• chr2-232444838-G-C

Variant summary

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

The ENST00000509197.1(DIS3L2P1):​n.74-29G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 154,428 control chromosomes in the GnomAD database, including 24,287 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 (23803 hom., cov: 33)
  • Exomes 𝑓: 0.62 (484 hom.)
• Consequence: DIS3L2P1 ENST00000509197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

DIS3L2P1 (HGNC:14021): (DIS3 like 3'-5' exoribonuclease 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIS3L2P1	ENST00000509197.1	n.74-29G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84643 AN: 151918 Hom.: 23782 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.622 AC: 1487 AN: 2392 Hom.: 484 Cov.: 0 AF XY: 0.608 AC XY: 801 AN XY: 1318

Gnomad4 AFR exome AF: 0.609

Gnomad4 AMR exome AF: 0.559

Gnomad4 ASJ exome AF: 0.833

Gnomad4 EAS exome AF: 0.667

Gnomad4 SAS exome AF: 0.712

Gnomad4 FIN exome AF: 0.569

Gnomad4 NFE exome AF: 0.527

Gnomad4 OTH exome AF: 0.580

GnomAD4 genome AF: 0.557 AC: 84704 AN: 152036 Hom.: 23803 Cov.: 33 AF XY: 0.559 AC XY: 41517 AN XY: 74310

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.567

Alfa AF: 0.544 Hom.: 26200

Bravo AF: 0.559

Asia WGS AF: 0.656 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs790040; hg19: chr2-233309548;