NM_001098511.3:c.335-10_335-9delTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001098511.3(KIF2A):c.335-10_335-9delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 967,854 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KIF2A
NM_001098511.3 intron
NM_001098511.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0840
Publications
0 publications found
Genes affected
KIF2A (HGNC:6318): (kinesin family member 2A) The protein encoded by this gene is a plus end-directed motor required for normal mitotic progression. The encoded protein is required for normal spindle activity during mitosis and is necessary for normal brain development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
DIMT1 (HGNC:30217): (DIM1 rRNA methyltransferase and ribosome maturation factor) The protein encoded by this gene is a methyltransferase that is responsible for dimethylation of adjacent adenosines near the 18S rRNA decoding site. The encoded protein is essential for ribosome biogenesis, although its catalytic activity is not involved in the process. The yeast ortholog of this protein functions in the cytoplasm while this protein functions in the nucleus. [provided by RefSeq, Jan 2017]
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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 |
|---|---|---|---|---|---|---|---|---|
| KIF2A | NM_001098511.3 | c.335-10_335-9delTT | intron_variant | Intron 4 of 20 | ENST00000407818.8 | NP_001091981.1 | ||
| KIF2A | NM_004520.5 | c.335-10_335-9delTT | intron_variant | Intron 4 of 19 | NP_004511.2 | |||
| KIF2A | NM_001243953.2 | c.335-10_335-9delTT | intron_variant | Intron 4 of 19 | NP_001230882.1 | |||
| KIF2A | NM_001243952.2 | c.254-10_254-9delTT | intron_variant | Intron 5 of 20 | NP_001230881.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| KIF2A | ENST00000407818.8 | c.335-20_335-19delTT | intron_variant | Intron 4 of 20 | 1 | NM_001098511.3 | ENSP00000385000.3 | |||
| ENSG00000288643 | ENST00000509663.2 | n.64+46032_64+46033delTT | intron_variant | Intron 1 of 5 | 3 | ENSP00000502199.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 148144Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
148144
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
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Gnomad AMR
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Gnomad ASJ
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Gnomad FIN
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.000652 AC: 30AN: 45996 AF XY: 0.000478 show subpopulations
GnomAD2 exomes
AF:
AC:
30
AN:
45996
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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Gnomad OTH exome
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GnomAD4 exome AF: 0.000119 AC: 115AN: 967854Hom.: 0 AF XY: 0.000126 AC XY: 60AN XY: 477874 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
115
AN:
967854
Hom.:
AF XY:
AC XY:
60
AN XY:
477874
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:
20348
American (AMR)
AF:
AC:
10
AN:
18410
Ashkenazi Jewish (ASJ)
AF:
AC:
2
AN:
16454
East Asian (EAS)
AF:
AC:
5
AN:
24306
South Asian (SAS)
AF:
AC:
15
AN:
51824
European-Finnish (FIN)
AF:
AC:
4
AN:
36086
Middle Eastern (MID)
AF:
AC:
2
AN:
4320
European-Non Finnish (NFE)
AF:
AC:
68
AN:
756214
Other (OTH)
AF:
AC:
6
AN:
39892
⚠️ 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: 0.239
Heterozygous variant carriers
0
19
39
58
78
97
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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2
4
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Age
GnomAD4 genome 0.00 AC: 0AN: 148144Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72060
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
148144
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
72060
African (AFR)
AF:
AC:
0
AN:
40564
American (AMR)
AF:
AC:
0
AN:
14812
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3414
East Asian (EAS)
AF:
AC:
0
AN:
5112
South Asian (SAS)
AF:
AC:
0
AN:
4704
European-Finnish (FIN)
AF:
AC:
0
AN:
9602
Middle Eastern (MID)
AF:
AC:
0
AN:
308
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66694
Other (OTH)
AF:
AC:
0
AN:
2026
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
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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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