2-232444316-G-C

Position:

• chr2-232444316-G-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 0.531 in 151,966 control chromosomes in the GnomAD database, including 21,649 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 0.53 (21649 hom., cov: 32)
• Consequence: DIS3L2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

Genes affected

DIS3L2P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIS3L2P1		n.232444316G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIS3L2P1	ENST00000509197.1	n.74-551G>C		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80604 AN: 151848 Hom.: 21631 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.531 AC: 80659 AN: 151966 Hom.: 21649 Cov.: 32 AF XY: 0.534 AC XY: 39649 AN XY: 74276

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.551

Alfa AF: 0.406 Hom.: 1116

Bravo AF: 0.529

Asia WGS AF: 0.646 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs790039; hg19: chr2-233309026;