dbSNP rs55781386: ECEL1P2:n.687C>G (chr2-232386358-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000461596.1(ECEL1P2):n.687C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 224,926 control chromosomes in the GnomAD database, including 5,716 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 0.20 ( 3741 hom., cov: 32)

Exomes 𝑓: 0.22 ( 1975 hom. )

Consequence

ECEL1P2
ENST00000461596.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.824

Publications

6 publications found

Variant links:

Genes affected

ECEL1P2 (HGNC:):

ECEL1P2 links:

ECEL1P2 (HGNC:14019): (endothelin converting enzyme like 1 pseudogene 2)

ECEL1P2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ECEL1P2	NR_028501.1 link	n.687C>G		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ECEL1P2	ENST00000461596.1 link	n.687C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ECEL1P2	ENST00000715297.1 link	n.173+342C>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30480

AN:

151994

Hom.:

3738

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0763

Gnomad AMI

AF:

0.484

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.0959

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.276

Gnomad OTH

AF:

0.229

GnomAD4 exome

AF:

0.217

AC:

15771

AN:

72814

Hom.:

1975

Cov.:

AF XY:

0.211

AC XY:

8009

AN XY:

37878

show subpopulations

African (AFR)

AF:

0.0458

AC:

AN:

982

American (AMR)

AF:

0.180

AC:

688

AN:

3832

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

441

AN:

1710

East Asian (EAS)

AF:

0.0859

AC:

163

AN:

1898

South Asian (SAS)

AF:

0.169

AC:

1822

AN:

10756

European-Finnish (FIN)

AF:

0.185

AC:

687

AN:

3712

Middle Eastern (MID)

AF:

0.244

AC:

AN:

312

European-Non Finnish (NFE)

AF:

0.241

AC:

10964

AN:

45438

Other (OTH)

AF:

0.212

AC:

885

AN:

4174

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

568

1137

1705

2274

2842

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

156

234

312

390

<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:

0.200

AC:

30486

AN:

152112

Hom.:

3741

Cov.:

AF XY:

0.198

AC XY:

14739

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.0765

AC:

3177

AN:

41542

American (AMR)

AF:

0.183

AC:

2804

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

1029

AN:

3472

East Asian (EAS)

AF:

0.0957

AC:

495

AN:

5170

South Asian (SAS)

AF:

0.193

AC:

921

AN:

4782

European-Finnish (FIN)

AF:

0.218

AC:

2312

AN:

10588

Middle Eastern (MID)

AF:

0.284

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.276

AC:

18744

AN:

67966

Other (OTH)

AF:

0.228

AC:

480

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1210

2421

3631

4842

6052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<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:

0.228

Hom.:

531

Bravo

AF:

0.194

Asia WGS

AF:

0.136

AC:

475

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

9.7

(source)

DANN

Benign

0.82

PhyloP100

0.82

Splicing

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