rs754314

Variant names:

• chr14-56285879-G-A
• rs754314
• NM_021255.3:c.310-2558G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-56285879-G-A
• chr14-56285879-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021255.3(PELI2):​c.310-2558G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0737 in 152,148 control chromosomes in the GnomAD database, including 564 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 0.074 (564 hom., cov: 32)
• Consequence: PELI2 NM_021255.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 2 publications found

Genes affected

PELI2 (HGNC:8828): (pellino E3 ubiquitin protein ligase family member 2) Predicted to enable protein-macromolecule adaptor activity and ubiquitin protein ligase activity. Acts upstream of or within positive regulation of MAPK cascade and positive regulation of protein phosphorylation. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021255.3. 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
	PELI2	NM_021255.3	MANE Select	c.310-2558G>A		intron	N/A	NP_067078.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PELI2	ENST00000267460.9	TSL:1 MANE Select	c.310-2558G>A		intron	N/A	ENSP00000267460.4
	PELI2	ENST00000705193.1		c.481-2558G>A		intron	N/A	ENSP00000516089.1
	PELI2	ENST00000559044.5	TSL:4	c.10-2558G>A		intron	N/A	ENSP00000452666.1

Frequencies

GnomAD3 genomes AF: 0.0737 AC: 11201 AN: 152030 Hom.: 565 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0521

Gnomad OTH AF: 0.0542

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

GnomAD4 genome AF: 0.0737 AC: 11217 AN: 152148 Hom.: 564 Cov.: 32 AF XY: 0.0735 AC XY: 5470 AN XY: 74376

African (AFR) AF: 0.117 AC: 4845 AN: 41496

American (AMR) AF: 0.0355 AC: 543 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3470

East Asian (EAS) AF: 0.224 AC: 1153 AN: 5158

South Asian (SAS) AF: 0.0934 AC: 450 AN: 4820

European-Finnish (FIN) AF: 0.0339 AC: 359 AN: 10596

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0521 AC: 3544 AN: 68006

Other (OTH) AF: 0.0579 AC: 122 AN: 2108

Alfa AF: 0.0647 Hom.: 46

Bravo AF: 0.0754

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs754314; hg19: chr14-56752597;