2-232446505-T-C

Variant names:

• chr2-232446505-T-C
• rs2697794

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 0.369 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
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 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.403-757T>C		intron	N/A
	ENSG00000306068	ENST00000815078.1		n.258+819T>C		intron	N/A
	ENSG00000306068	ENST00000815079.1		n.365+819T>C		intron	N/A

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

African (AFR) AF: 0.257 AC: 10491 AN: 40824

American (AMR) AF: 0.317 AC: 4776 AN: 15058

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1701 AN: 3424

East Asian (EAS) AF: 0.313 AC: 1577 AN: 5044

South Asian (SAS) AF: 0.368 AC: 1686 AN: 4578

European-Finnish (FIN) AF: 0.345 AC: 3546 AN: 10284

Middle Eastern (MID) AF: 0.486 AC: 140 AN: 288

European-Non Finnish (NFE) AF: 0.447 AC: 29773 AN: 66680

Other (OTH) AF: 0.399 AC: 826 AN: 2070

Alfa AF: 0.188 Hom.: 312

Bravo AF: 0.365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.046
DANN	Benign	0.27
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2697794; hg19: chr2-233311215;