dbSNP rs3748971: ECEL1P2:n.1072G>A (chr2-232385973-C-T) – 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.1072G>A 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 0.0598 in 152,286 control chromosomes in the GnomAD database, including 367 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 0.060 ( 366 hom., cov: 32)

Exomes 𝑓: 0.067 ( 1 hom. )

Consequence

ECEL1P2
ENST00000461596.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Publications

8 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 (EAS) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ECEL1P2	NR_028501.1 link	n.1072G>A		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.1072G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ECEL1P2	ENST00000715297.1 link	n.173+727G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.0598

AC:

9101

AN:

152078

Hom.:

366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0130

Gnomad AMI

AF:

0.0559

Gnomad AMR

AF:

0.0489

Gnomad ASJ

AF:

0.0919

Gnomad EAS

AF:

0.0912

Gnomad SAS

AF:

0.0740

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0786

Gnomad OTH

AF:

0.0540

GnomAD4 exome

AF:

0.0667

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0682

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0606

AC:

AN:

Other (OTH)

AF:

0.100

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0598

AC:

9095

AN:

152196

Hom.:

366

Cov.:

AF XY:

0.0610

AC XY:

4537

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0130

AC:

542

AN:

41548

American (AMR)

AF:

0.0489

AC:

747

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0919

AC:

319

AN:

3470

East Asian (EAS)

AF:

0.0908

AC:

471

AN:

5188

South Asian (SAS)

AF:

0.0742

AC:

355

AN:

4782

European-Finnish (FIN)

AF:

0.108

AC:

1141

AN:

10602

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0785

AC:

5339

AN:

67994

Other (OTH)

AF:

0.0534

AC:

113

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

432

863

1295

1726

2158

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0708

Hom.:

797

Bravo

AF:

0.0535

Asia WGS

AF:

0.0730

AC:

253

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

3.4

(source)

DANN

Benign

0.83

PhyloP100

0.30

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