14-56150938-G-T

Variant names:

• chr14-56150938-G-T
• rs242407
• NM_021255.3:c.78-27397G>T

Variant summary

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

The NM_021255.3(PELI2):​c.78-27397G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0752 in 152,240 control chromosomes in the GnomAD database, including 789 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 0.075 (789 hom., cov: 32)
• Consequence: PELI2 NM_021255.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PELI2	NM_021255.3	c.78-27397G>T		intron_variant	Intron 1 of 5	ENST00000267460.9	NP_067078.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PELI2	ENST00000267460.9	c.78-27397G>T		intron_variant	Intron 1 of 5	1	NM_021255.3	ENSP00000267460.4
PELI2	ENST00000705193.1	c.249-27397G>T		intron_variant	Intron 1 of 5			ENSP00000516089.1
PELI2	ENST00000559044.5	c.-223-27397G>T		intron_variant	Intron 1 of 4	4		ENSP00000452666.1
PELI2	ENST00000561019.1	c.-223-27397G>T		intron_variant	Intron 1 of 4	5		ENSP00000453988.1

Frequencies

GnomAD3 genomes AF: 0.0752 AC: 11433 AN: 152120 Hom.: 783 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0677

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0752 AC: 11445 AN: 152240 Hom.: 789 Cov.: 32 AF XY: 0.0824 AC XY: 6134 AN XY: 74426

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0677

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0745 Hom.: 70

Bravo AF: 0.0723

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.51

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

Publications

LitVar

Other links and lift over

dbSNP: rs242407; hg19: chr14-56617656;