rs6733160

Positions:

• chr2-64137498-T-C
• chr2-64137498-T-G

Variant summary

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

The NM_020651.4(PELI1):​c.-70+6583A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,978 control chromosomes in the GnomAD database, including 33,523 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 0.64 (33523 hom., cov: 31)
• Consequence: PELI1 NM_020651.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

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]

PELI1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PELI1	NM_020651.4	c.-70+6583A>G		intron_variant		ENST00000358912.5	NP_065702.2
PELI1	XM_011532994.4	c.-15168A>G		5_prime_UTR_variant	1/7		XP_011531296.1
PELI1	XM_017004520.2	c.-70+5820A>G		intron_variant			XP_016860009.1
PELI1	XM_047445137.1	c.-180+5820A>G		intron_variant			XP_047301093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PELI1	ENST00000358912.5	c.-70+6583A>G		intron_variant		1	NM_020651.4	ENSP00000351789.4
PELI1	ENST00000466177.6	n.282+6583A>G		intron_variant		5
PELI1	ENST00000468869.2	n.525+5820A>G		intron_variant		4
PELI1	ENST00000494203.1	n.340+6583A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97371 AN: 151860 Hom.: 33474 Cov.: 31

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.641 AC: 97483 AN: 151978 Hom.: 33523 Cov.: 31 AF XY: 0.640 AC XY: 47485 AN XY: 74248

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.620

Alfa AF: 0.597 Hom.: 4221

Bravo AF: 0.668

Asia WGS AF: 0.792 AC: 2754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.27
DANN	Benign	0.43

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: rs6733160; hg19: chr2-64364632;