2-232378254-G-A

Variant summary

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

The ENST00000715297.1(ECEL1P2):​n.812+691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,938 control chromosomes in the GnomAD database, including 15,146 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 0.44 ( 15146 hom., cov: 32)

Consequence

ECEL1P2
ENST00000715297.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0590

Publications

7 publications found
Variant links:
Genes affected

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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124906123XR_007088121.1 linkn.88+691C>T intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ECEL1P2ENST00000715297.1 linkn.812+691C>T intron_variant Intron 4 of 6

Frequencies

GnomAD3 genomes
AF:
0.439
AC:
66602
AN:
151820
Hom.:
15133
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.330
Gnomad AMI
AF:
0.331
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.606
Gnomad SAS
AF:
0.536
Gnomad FIN
AF:
0.547
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.446
Gnomad OTH
AF:
0.439
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.439
AC:
66629
AN:
151938
Hom.:
15146
Cov.:
32
AF XY:
0.445
AC XY:
33064
AN XY:
74274
show subpopulations
African (AFR)
AF:
0.329
AC:
13634
AN:
41442
American (AMR)
AF:
0.531
AC:
8111
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.503
AC:
1745
AN:
3468
East Asian (EAS)
AF:
0.606
AC:
3114
AN:
5142
South Asian (SAS)
AF:
0.535
AC:
2579
AN:
4820
European-Finnish (FIN)
AF:
0.547
AC:
5792
AN:
10584
Middle Eastern (MID)
AF:
0.483
AC:
141
AN:
292
European-Non Finnish (NFE)
AF:
0.446
AC:
30287
AN:
67898
Other (OTH)
AF:
0.440
AC:
926
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.493
Heterozygous variant carriers
0
1818
3637
5455
7274
9092
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
630
1260
1890
2520
3150
<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:
0.455
Hom.:
13672
Bravo
AF:
0.436
Asia WGS
AF:
0.594
AC:
2061
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.1
DANN
Benign
0.69
PhyloP100
0.059
PromoterAI
-0.026
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs2014683; hg19: chr2-233242964; API