GeneBe

1-189502601-TAAAAAAAAAAA-TAAAAAAAAAAAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The XR_002958413.2(LOC105371657):​n.483-65710_483-65709dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 107,828 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 31)

Consequence

LOC105371657
XR_002958413.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

0 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105371657XR_002958413.2 linkn.483-65710_483-65709dupAA intron_variant Intron 3 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.00119
AC:
128
AN:
107824
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00430
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00103
Gnomad ASJ
AF:
0.000372
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000295
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000383
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00119
AC:
128
AN:
107828
Hom.:
0
Cov.:
31
AF XY:
0.00124
AC XY:
64
AN XY:
51752
show subpopulations
African (AFR)
AF:
0.00429
AC:
113
AN:
26336
American (AMR)
AF:
0.00102
AC:
11
AN:
10742
Ashkenazi Jewish (ASJ)
AF:
0.000372
AC:
1
AN:
2688
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3886
South Asian (SAS)
AF:
0.000296
AC:
1
AN:
3376
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
6106
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
188
European-Non Finnish (NFE)
AF:
0.0000383
AC:
2
AN:
52244
Other (OTH)
AF:
0.00
AC:
0
AN:
1496
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.446
Heterozygous variant carriers
0
6
12
18
24
30
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
4
8
12
16
20
<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:
0.00
Hom.:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-1.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs35854821; hg19: chr1-189471731; API