NM_001242957.3:c.*601delT
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS1
The NM_001242957.3(MAK):c.*601delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0016 ( 0 hom., cov: 0)
Exomes 𝑓: 0.11 ( 0 hom. )
Consequence
MAK
NM_001242957.3 3_prime_UTR
NM_001242957.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.957
Publications
0 publications found
Genes affected
MAK (HGNC:6816): (male germ cell associated kinase) The product of this gene is a serine/threonine protein kinase related to kinases involved in cell cycle regulation. Studies of the mouse and rat homologs have localized the kinase to the chromosomes during meiosis in spermatogenesis, specifically to the synaptonemal complex that exists while homologous chromosomes are paired. Mutations in this gene have been associated with ciliary defects resulting in retinitis pigmentosa 62. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
TMEM14B (HGNC:21384): (transmembrane protein 14B) Enables identical protein binding activity. Involved in cerebral cortex development; neural precursor cell proliferation; and regulation of G1/S transition of mitotic cell cycle. Predicted to be integral component of membrane. Predicted to be active in mitochondrial inner membrane. [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 -4 ACMG points.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00159 (218/137534) while in subpopulation AFR AF = 0.00421 (151/35830). AF 95% confidence interval is 0.00367. There are 0 homozygotes in GnomAd4. There are 103 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001242957.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| MAK | NM_001242957.3 | MANE Select | c.*601delT | 3_prime_UTR | Exon 15 of 15 | NP_001229886.1 | P20794-2 | ||
| MAK | NM_005906.6 | c.*601delT | 3_prime_UTR | Exon 14 of 14 | NP_005897.1 | A0A140VK28 | |||
| MAK | NM_001242385.2 | c.*601delT | 3_prime_UTR | Exon 13 of 13 | NP_001229314.1 | P20794-3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MAK | ENST00000354489.7 | TSL:5 MANE Select | c.*601delT | 3_prime_UTR | Exon 15 of 15 | ENSP00000346484.3 | P20794-2 | ||
| MAK | ENST00000474039.5 | TSL:1 | c.*601delT | 3_prime_UTR | Exon 14 of 14 | ENSP00000476067.1 | P20794-1 | ||
| MAK | ENST00000536370.6 | TSL:1 | c.*601delT | 3_prime_UTR | Exon 13 of 13 | ENSP00000442221.2 | P20794-3 |
Frequencies
GnomAD3 genomes 0.00157 AC: 216AN: 137526Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
216
AN:
137526
Hom.:
Cov.:
0
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: 0.114 AC: 5AN: 44Hom.: 0 Cov.: 0 AF XY: 0.0714 AC XY: 2AN XY: 28 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
5
AN:
44
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
28
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
2
AN:
8
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
AC:
1
AN:
10
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
2
AN:
24
Other (OTH)
AF:
AC:
0
AN:
2
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000257297), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.335
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00159 AC: 218AN: 137534Hom.: 0 Cov.: 0 AF XY: 0.00155 AC XY: 103AN XY: 66248 show subpopulations
GnomAD4 genome
AF:
AC:
218
AN:
137534
Hom.:
Cov.:
0
AF XY:
AC XY:
103
AN XY:
66248
show subpopulations
African (AFR)
AF:
AC:
151
AN:
35830
American (AMR)
AF:
AC:
15
AN:
13784
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3304
East Asian (EAS)
AF:
AC:
1
AN:
4818
South Asian (SAS)
AF:
AC:
0
AN:
4448
European-Finnish (FIN)
AF:
AC:
12
AN:
7664
Middle Eastern (MID)
AF:
AC:
0
AN:
260
European-Non Finnish (NFE)
AF:
AC:
37
AN:
64680
Other (OTH)
AF:
AC:
2
AN:
1866
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.455
Heterozygous variant carriers
0
9
19
28
38
47
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:
Hom.:
ClinVar
Not reported inComputational 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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.