chr14-56216743-G-A

Variant names:

• chr14-56216743-G-A
• rs12432184
• NM_021255.3:c.207+38279G>A

Variant summary

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

The NM_021255.3(PELI2):​c.207+38279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,042 control chromosomes in the GnomAD database, including 13,036 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 0.40 (13036 hom., cov: 33)
• Consequence: PELI2 NM_021255.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.517 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.207+38279G>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.207+38279G>A		intron	N/A	ENSP00000267460.4
	PELI2	ENST00000705193.1		c.378+38279G>A		intron	N/A	ENSP00000516089.1
	PELI2	ENST00000559044.5	TSL:4	c.-94+38279G>A		intron	N/A	ENSP00000452666.1

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60844 AN: 151924 Hom.: 13033 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.400 AC: 60869 AN: 152042 Hom.: 13036 Cov.: 33 AF XY: 0.406 AC XY: 30204 AN XY: 74314

African (AFR) AF: 0.233 AC: 9668 AN: 41484

American (AMR) AF: 0.479 AC: 7323 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1712 AN: 5176

South Asian (SAS) AF: 0.534 AC: 2580 AN: 4834

European-Finnish (FIN) AF: 0.491 AC: 5166 AN: 10532

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31351 AN: 67962

Other (OTH) AF: 0.432 AC: 910 AN: 2108

Alfa AF: 0.424 Hom.: 2522

Bravo AF: 0.393

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.59
PhyloP100		0.29
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: rs12432184; hg19: chr14-56683461;