chr2-64093612-G-A

Position:

• chr2-64093612-G-A

Variant summary

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

The NM_020651.4(PELI1):​c.*1090C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,624 control chromosomes in the GnomAD database, including 971 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 0.11 (968 hom., cov: 32)
  • Exomes 𝑓: 0.10 (3 hom.)
• Consequence: PELI1 NM_020651.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793

Genes affected

PELI1 (HGNC:8827): (pellino E3 ubiquitin protein ligase 1) Enables ubiquitin protein ligase activity. Involved in several processes, including negative regulation of necroptotic process; protein polyubiquitination; and response to lipopolysaccharide. Predicted to be located in cytosol. [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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PELI1	NM_020651.4	c.*1090C>T		3_prime_UTR_variant	7/7	ENST00000358912.5	NP_065702.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PELI1	ENST00000358912.5	c.*1090C>T		3_prime_UTR_variant	7/7	1	NM_020651.4	ENSP00000351789.4

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16317 AN: 152068 Hom.: 967 Cov.: 32

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0989

GnomAD4 exome AF: 0.100 AC: 44 AN: 438 Hom.: 3 Cov.: 0 AF XY: 0.0902 AC XY: 24 AN XY: 266

Gnomad4 FIN exome AF: 0.104

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.107 AC: 16320 AN: 152186 Hom.: 968 Cov.: 32 AF XY: 0.107 AC XY: 7987 AN XY: 74418

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0860

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0900

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.118 Hom.: 1554

Bravo AF: 0.110

Asia WGS AF: 0.110 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10496105; hg19: chr2-64320746;