rs6733160

Variant names:

• chr2-64137498-T-C
• rs6733160
• NM_020651.4:c.-70+6583A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020651.4. 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
	PELI1	NM_020651.4	MANE Select	c.-70+6583A>G		intron	N/A	NP_065702.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PELI1	ENST00000358912.5	TSL:1 MANE Select	c.-70+6583A>G		intron	N/A	ENSP00000351789.4
	PELI1	ENST00000466177.6	TSL:5	n.282+6583A>G		intron	N/A
	PELI1	ENST00000468869.2	TSL:4	n.525+5820A>G		intron	N/A

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

African (AFR) AF: 0.884 AC: 36649 AN: 41458

American (AMR) AF: 0.632 AC: 9655 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2057 AN: 3468

East Asian (EAS) AF: 0.860 AC: 4459 AN: 5184

South Asian (SAS) AF: 0.679 AC: 3268 AN: 4812

European-Finnish (FIN) AF: 0.453 AC: 4763 AN: 10520

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34536 AN: 67948

Other (OTH) AF: 0.620 AC: 1308 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.27
DANN	Benign	0.43
PhyloP100		-3.4
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: rs6733160; hg19: chr2-64364632;