2-232446505-T-C

Position:

• chr2-232446505-T-C

Variant summary

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

The variant allele was found at a frequency of 0.369 in 149,120 control chromosomes in the GnomAD database, including 10,846 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 0.37 (10846 hom., cov: 29)
• Consequence: DIS3L2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

DIS3L2P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIS3L2P1		n.232446505T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIS3L2P1	ENST00000509197.1	n.403-757T>C		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.370 AC: 55060 AN: 149006 Hom.: 10842 Cov.: 29

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.369 AC: 55071 AN: 149120 Hom.: 10846 Cov.: 29 AF XY: 0.362 AC XY: 26344 AN XY: 72754

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.399

Alfa AF: 0.188 Hom.: 312

Bravo AF: 0.365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.046
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2697794; hg19: chr2-233311215;