GeneBe

ENST00000546177.1:n.198+21711G>A

Variant names:

Variant summary

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

The ENST00000546177.1(JRKL):​n.198+21711G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,928 control chromosomes in the GnomAD database, including 35,538 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 0.68 ( 35538 hom., cov: 30)

Consequence

JRKL
ENST00000546177.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Publications

0 publications found
Variant links:
Genes affected
JRKL (HGNC:6200): (JRK like) The function of this gene has not yet been defined, however, the encoded protein shares similarity with the human (41% identical) and mouse (34% identical) jerky gene products. This protein may act as a nuclear regulatory protein. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2012]

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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
JRKLENST00000546177.1 linkn.198+21711G>A intron_variant Intron 2 of 2 1

Frequencies

GnomAD3 genomes
AF:
0.678
AC:
102915
AN:
151808
Hom.:
35505
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.767
Gnomad AMI
AF:
0.692
Gnomad AMR
AF:
0.581
Gnomad ASJ
AF:
0.737
Gnomad EAS
AF:
0.359
Gnomad SAS
AF:
0.557
Gnomad FIN
AF:
0.657
Gnomad MID
AF:
0.674
Gnomad NFE
AF:
0.678
Gnomad OTH
AF:
0.684
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.678
AC:
103003
AN:
151928
Hom.:
35538
Cov.:
30
AF XY:
0.673
AC XY:
49943
AN XY:
74248
show subpopulations
African (AFR)
AF:
0.767
AC:
31787
AN:
41440
American (AMR)
AF:
0.580
AC:
8860
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.737
AC:
2555
AN:
3468
East Asian (EAS)
AF:
0.359
AC:
1855
AN:
5164
South Asian (SAS)
AF:
0.556
AC:
2671
AN:
4804
European-Finnish (FIN)
AF:
0.657
AC:
6905
AN:
10514
Middle Eastern (MID)
AF:
0.687
AC:
202
AN:
294
European-Non Finnish (NFE)
AF:
0.678
AC:
46097
AN:
67954
Other (OTH)
AF:
0.682
AC:
1440
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1624
3248
4872
6496
8120
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
800
1600
2400
3200
4000
<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:
0.552
Hom.:
2346
Bravo
AF:
0.673
Asia WGS
AF:
0.515
AC:
1785
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.52
DANN
Benign
0.64
PhyloP100
-1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs10501853; hg19: chr11-96159266; API