2-232444316-G-C

Variant names:

• chr2-232444316-G-C
• rs790039

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ENSG00000306068 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509197.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIS3L2P1	ENST00000509197.1	TSL:6	n.74-551G>C		intron	N/A
	ENSG00000306068	ENST00000815078.1		n.22+521G>C		intron	N/A
	ENSG00000306068	ENST00000815079.1		n.129+311G>C		intron	N/A

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

African (AFR) AF: 0.512 AC: 21205 AN: 41438

American (AMR) AF: 0.547 AC: 8353 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1872 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3167 AN: 5156

South Asian (SAS) AF: 0.674 AC: 3245 AN: 4812

European-Finnish (FIN) AF: 0.536 AC: 5674 AN: 10580

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35431 AN: 67920

Other (OTH) AF: 0.551 AC: 1161 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs790039; hg19: chr2-233309026;