GeneBe

rs34808376

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000419225.1(EN2-DT):​n.110+973_110+974insGC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.49 ( 19443 hom., cov: 0)

Consequence

EN2-DT
ENST00000419225.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.561

Publications

1 publications found
Variant links:
Genes affected
EN2-DT (HGNC:55659): (EN2 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EN2-DTNR_186580.1 linkn.129+972_129+973dupGC intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EN2-DTENST00000419225.1 linkn.110+973_110+974insGC intron_variant Intron 1 of 2 4
EN2-DTENST00000781270.1 linkn.107+973_107+974insGC intron_variant Intron 1 of 4
EN2-DTENST00000781271.1 linkn.86+973_86+974insGC intron_variant Intron 1 of 4
EN2-DTENST00000781273.1 linkn.130+973_130+974insGC intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.494
AC:
74901
AN:
151610
Hom.:
19425
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.629
Gnomad AMI
AF:
0.339
Gnomad AMR
AF:
0.446
Gnomad ASJ
AF:
0.378
Gnomad EAS
AF:
0.810
Gnomad SAS
AF:
0.585
Gnomad FIN
AF:
0.400
Gnomad MID
AF:
0.392
Gnomad NFE
AF:
0.417
Gnomad OTH
AF:
0.468
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.494
AC:
74958
AN:
151728
Hom.:
19443
Cov.:
0
AF XY:
0.498
AC XY:
36896
AN XY:
74150
show subpopulations
African (AFR)
AF:
0.628
AC:
25931
AN:
41270
American (AMR)
AF:
0.445
AC:
6799
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.378
AC:
1312
AN:
3470
East Asian (EAS)
AF:
0.810
AC:
4160
AN:
5134
South Asian (SAS)
AF:
0.585
AC:
2820
AN:
4824
European-Finnish (FIN)
AF:
0.400
AC:
4215
AN:
10542
Middle Eastern (MID)
AF:
0.377
AC:
110
AN:
292
European-Non Finnish (NFE)
AF:
0.417
AC:
28318
AN:
67924
Other (OTH)
AF:
0.469
AC:
985
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1879
3758
5638
7517
9396
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
666
1332
1998
2664
3330
<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:
0.460
Hom.:
1740
Bravo
AF:
0.497
Asia WGS
AF:
0.655
AC:
2279
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.56

Splicing

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

Publications

Other links and lift over

dbSNP: rs34808376; hg19: chr7-155248711; API