11-30214997-T-C

Variant summary

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

The ENST00000527819.2(ARL14EP-DT):​n.471-58144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,016 control chromosomes in the GnomAD database, including 17,673 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 0.48 ( 17673 hom., cov: 32)

Consequence

ARL14EP-DT
ENST00000527819.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.789

Publications

11 publications found
Variant links:
Genes affected
ARL14EP-DT (HGNC:55517): (ARL14EP divergent transcript)

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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARL14EP-DTNR_187431.1 linkn.250+101893A>G intron_variant Intron 3 of 3
ARL14EP-DTNR_187432.1 linkn.429+101893A>G intron_variant Intron 3 of 3
ARL14EP-DTNR_187433.1 linkn.250+101893A>G intron_variant Intron 3 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARL14EP-DTENST00000527819.2 linkn.471-58144A>G intron_variant Intron 3 of 5 3
ARL14EP-DTENST00000662729.1 linkn.293-58144A>G intron_variant Intron 3 of 4
ARL14EP-DTENST00000726808.1 linkn.517-58144A>G intron_variant Intron 3 of 4
ARL14EP-DTENST00000726809.1 linkn.375-53949A>G intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.477
AC:
72464
AN:
151898
Hom.:
17656
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.563
Gnomad AMI
AF:
0.273
Gnomad AMR
AF:
0.494
Gnomad ASJ
AF:
0.438
Gnomad EAS
AF:
0.672
Gnomad SAS
AF:
0.574
Gnomad FIN
AF:
0.490
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.402
Gnomad OTH
AF:
0.457
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.477
AC:
72522
AN:
152016
Hom.:
17673
Cov.:
32
AF XY:
0.484
AC XY:
35948
AN XY:
74330
show subpopulations
African (AFR)
AF:
0.563
AC:
23341
AN:
41444
American (AMR)
AF:
0.494
AC:
7547
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.438
AC:
1521
AN:
3470
East Asian (EAS)
AF:
0.672
AC:
3474
AN:
5168
South Asian (SAS)
AF:
0.574
AC:
2759
AN:
4808
European-Finnish (FIN)
AF:
0.490
AC:
5182
AN:
10574
Middle Eastern (MID)
AF:
0.507
AC:
149
AN:
294
European-Non Finnish (NFE)
AF:
0.402
AC:
27341
AN:
67966
Other (OTH)
AF:
0.454
AC:
960
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1938
3875
5813
7750
9688
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
660
1320
1980
2640
3300
<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:
0.431
Hom.:
7187
Bravo
AF:
0.482
Asia WGS
AF:
0.569
AC:
1977
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.27
DANN
Benign
0.48
PhyloP100
-0.79

Splicing

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

Publications

Other links and lift over

dbSNP: rs555621; hg19: chr11-30236544; API