NM_007317.3:c.24G>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_007317.3(KIF22):c.24G>A(p.Gln8Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,601,918 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
KIF22
NM_007317.3 synonymous
NM_007317.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0180
Publications
0 publications found
Genes affected
KIF22 (HGNC:6391): (kinesin family member 22) The protein encoded by this gene is a member of the kinesin-like protein family. The family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. The C-terminal half of this protein has been shown to bind DNA. Studies with the Xenopus homolog suggests its essential role in metaphase chromosome alignment and maintenance. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
KIF22 Gene-Disease associations (from GenCC):
- spondyloepimetaphyseal dysplasia with multiple dislocationsInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP7
Synonymous conserved (PhyloP=-0.018 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_007317.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| KIF22 | NM_007317.3 | MANE Select | c.24G>A | p.Gln8Gln | synonymous | Exon 1 of 14 | NP_015556.1 | Q14807-1 | |
| KIF22 | NM_001256269.2 | c.-230G>A | 5_prime_UTR | Exon 1 of 15 | NP_001243198.1 | Q14807-2 | |||
| KIF22 | NM_001256270.1 | c.-573G>A | upstream_gene | N/A | NP_001243199.1 | Q14807-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KIF22 | ENST00000160827.9 | TSL:1 MANE Select | c.24G>A | p.Gln8Gln | synonymous | Exon 1 of 14 | ENSP00000160827.5 | Q14807-1 | |
| KIF22 | ENST00000569382.3 | TSL:5 | c.24G>A | p.Gln8Gln | synonymous | Exon 1 of 14 | ENSP00000456165.3 | H3BRB3 | |
| KIF22 | ENST00000936369.1 | c.24G>A | p.Gln8Gln | synonymous | Exon 1 of 15 | ENSP00000606428.1 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152252
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1449666Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 719904 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1449666
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
719904
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
33322
American (AMR)
AF:
AC:
0
AN:
43128
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25840
East Asian (EAS)
AF:
AC:
0
AN:
39266
South Asian (SAS)
AF:
AC:
0
AN:
84294
European-Finnish (FIN)
AF:
AC:
0
AN:
51852
Middle Eastern (MID)
AF:
AC:
0
AN:
5730
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1106436
Other (OTH)
AF:
AC:
0
AN:
59798
⚠️ 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: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74380 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152252
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74380
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41460
American (AMR)
AF:
AC:
0
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5196
South Asian (SAS)
AF:
AC:
0
AN:
4838
European-Finnish (FIN)
AF:
AC:
0
AN:
10626
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68052
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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