2-201381221-TAAAAA-TAA
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_015049.3(TRAK2):c.2070-6_2070-4delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,374,814 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000063 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TRAK2
NM_015049.3 splice_region, intron
NM_015049.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.49
Publications
4 publications found
Genes affected
TRAK2 (HGNC:13206): (trafficking kinesin protein 2) Predicted to enable GABA receptor binding activity and myosin binding activity. Predicted to be involved in several processes, including mitochondrion distribution; organelle transport along microtubule; and protein targeting. Predicted to be located in cytoplasm and plasma membrane. Predicted to be active in cytoplasmic vesicle; dendrite; and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP6
Variant 2-201381221-TAAA-T is Benign according to our data. Variant chr2-201381221-TAAA-T is described in ClinVar as Benign. ClinVar VariationId is 2744220.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_015049.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TRAK2 | NM_015049.3 | MANE Select | c.2070-6_2070-4delTTT | splice_region intron | N/A | NP_055864.2 | O60296-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TRAK2 | ENST00000332624.8 | TSL:1 MANE Select | c.2070-6_2070-4delTTT | splice_region intron | N/A | ENSP00000328875.3 | O60296-1 | ||
| TRAK2 | ENST00000861749.1 | c.2139-6_2139-4delTTT | splice_region intron | N/A | ENSP00000531808.1 | ||||
| TRAK2 | ENST00000861746.1 | c.2070-6_2070-4delTTT | splice_region intron | N/A | ENSP00000531805.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 144836Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
144836
Hom.:
Cov.:
0
Gnomad AFR
AF:
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Gnomad OTH
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GnomAD2 exomes AF: 0.000260 AC: 46AN: 176994 AF XY: 0.000256 show subpopulations
GnomAD2 exomes
AF:
AC:
46
AN:
176994
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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GnomAD4 exome AF: 0.0000626 AC: 86AN: 1374814Hom.: 0 AF XY: 0.0000708 AC XY: 48AN XY: 677710 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
86
AN:
1374814
Hom.:
AF XY:
AC XY:
48
AN XY:
677710
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
3
AN:
29366
American (AMR)
AF:
AC:
8
AN:
30776
Ashkenazi Jewish (ASJ)
AF:
AC:
5
AN:
22732
East Asian (EAS)
AF:
AC:
2
AN:
37800
South Asian (SAS)
AF:
AC:
17
AN:
75182
European-Finnish (FIN)
AF:
AC:
2
AN:
50018
Middle Eastern (MID)
AF:
AC:
0
AN:
5254
European-Non Finnish (NFE)
AF:
AC:
48
AN:
1067420
Other (OTH)
AF:
AC:
1
AN:
56266
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.273
Heterozygous variant carriers
0
11
22
32
43
54
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
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Age
GnomAD4 genome 0.00 AC: 0AN: 144836Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 70452
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
144836
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
70452
African (AFR)
AF:
AC:
0
AN:
37680
American (AMR)
AF:
AC:
0
AN:
14570
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3410
East Asian (EAS)
AF:
AC:
0
AN:
4910
South Asian (SAS)
AF:
AC:
0
AN:
4714
European-Finnish (FIN)
AF:
AC:
0
AN:
9820
Middle Eastern (MID)
AF:
AC:
0
AN:
300
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66574
Other (OTH)
AF:
AC:
0
AN:
1992
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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