dbSNP rs2277302: PELI3:p.Asp209Asp (chr11-66473411-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_145065.3(PELI3):c.627T>C(p.Asp209Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,612,418 control chromosomes in the GnomAD database, including 50,539 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 0.27 ( 5993 hom., cov: 32)

Exomes 𝑓: 0.24 ( 44546 hom. )

Consequence

PELI3
NM_145065.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0530

Publications

25 publications found

Variant links:

Genes affected

PELI3 (HGNC:30010): (pellino E3 ubiquitin protein ligase family member 3) The protein encoded by this gene is a scaffold protein and an intermediate signaling protein in the innate immune response pathway. The encoded protein helps transmit the immune response signal from Toll-like receptors to IRAK1/TRAF6 complexes. Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2011]

PELI3 links:

DPP3-DT (HGNC:55494): (DPP3 divergent transcript)

DPP3-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP7

Synonymous conserved (PhyloP=0.053 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PELI3	NM_145065.3 link	c.627T>C	p.Asp209Asp	synonymous_variant	Exon 6 of 8	ENST00000320740.12	NP_659502.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PELI3	ENST00000320740.12 link	c.627T>C	p.Asp209Asp	synonymous_variant	Exon 6 of 8	1	NM_145065.3	ENSP00000322532.7		Q8N2H9-1

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41102

AN:

151986

Hom.:

5982

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.392

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.225

GnomAD2 exomes

AF:

0.239

AC:

59596

AN:

249160

AF XY:

0.238

show subpopulations

Gnomad AFR exome

AF:

0.336

Gnomad AMR exome

AF:

0.152

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.261

Gnomad FIN exome

AF:

0.385

Gnomad NFE exome

AF:

0.241

Gnomad OTH exome

AF:

0.216

GnomAD4 exome

AF:

0.243

AC:

354656

AN:

1460314

Hom.:

44546

Cov.:

AF XY:

0.242

AC XY:

175744

AN XY:

726428

show subpopulations

African (AFR)

AF:

0.339

AC:

11349

AN:

33446

American (AMR)

AF:

0.155

AC:

6934

AN:

44632

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

4298

AN:

26092

East Asian (EAS)

AF:

0.256

AC:

10170

AN:

39694

South Asian (SAS)

AF:

0.202

AC:

17387

AN:

86218

European-Finnish (FIN)

AF:

0.378

AC:

19936

AN:

52694

Middle Eastern (MID)

AF:

0.140

AC:

805

AN:

5768

European-Non Finnish (NFE)

AF:

0.243

AC:

269673

AN:

1111428

Other (OTH)

AF:

0.234

AC:

14104

AN:

60342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

14798

29597

44395

59194

73992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9186

18372

27558

36744

45930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.271

AC:

41145

AN:

152104

Hom.:

5993

Cov.:

AF XY:

0.273

AC XY:

20280

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.336

AC:

13933

AN:

41478

American (AMR)

AF:

0.189

AC:

2896

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

513

AN:

3470

East Asian (EAS)

AF:

0.258

AC:

1334

AN:

5172

South Asian (SAS)

AF:

0.190

AC:

914

AN:

4818

European-Finnish (FIN)

AF:

0.392

AC:

4144

AN:

10576

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.245

AC:

16671

AN:

67986

Other (OTH)

AF:

0.221

AC:

466

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1541

3081

4622

6162

7703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.241

Hom.:

10745

Bravo

AF:

0.258

Asia WGS

AF:

0.230

AC:

801

AN:

3478

EpiCase

AF:

0.225

EpiControl

AF:

0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.0

(source)

DANN

Benign

0.61

PhyloP100

0.053

PromoterAI

0.0072

Neutral

(source)

Mutation Taster

=97/3

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over