GeneBe

NM_153827.5:c.6C>G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_153827.5(MINK1):​c.6C>G​(p.Gly2Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000742 in 1,347,210 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. Synonymous variant affecting the same amino acid position (i.e. G2G) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 7.4e-7 ( 0 hom. )

Consequence

MINK1
NM_153827.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.256

Publications

0 publications found
Variant links:
Genes affected
MINK1 (HGNC:17565): (misshapen like kinase 1) This gene encodes a serine/threonine kinase belonging to the germinal center kinase (GCK) family. The protein is structurally similar to the kinases that are related to NIK and may belong to a distinct subfamily of NIK-related kinases within the GCK family. Studies of the mouse homolog indicate an up-regulation of expression in the course of postnatal mouse cerebral development and activation of the cJun N-terminal kinase (JNK) and the p38 pathways. [provided by RefSeq, Mar 2016]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP7
Synonymous conserved (PhyloP=0.256 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MINK1NM_153827.5 linkc.6C>G p.Gly2Gly synonymous_variant Exon 1 of 32 ENST00000355280.11 NP_722549.2 Q8N4C8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MINK1ENST00000355280.11 linkc.6C>G p.Gly2Gly synonymous_variant Exon 1 of 32 1 NM_153827.5 ENSP00000347427.6 Q8N4C8-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
7.42e-7
AC:
1
AN:
1347210
Hom.:
0
Cov.:
31
AF XY:
0.00000151
AC XY:
1
AN XY:
664348
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
27434
American (AMR)
AF:
0.00
AC:
0
AN:
32050
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
23908
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30040
South Asian (SAS)
AF:
0.00
AC:
0
AN:
75640
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
35036
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4300
European-Non Finnish (NFE)
AF:
9.41e-7
AC:
1
AN:
1062652
Other (OTH)
AF:
0.00
AC:
0
AN:
56150
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

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
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.37
CADD
Benign
15
DANN
Benign
0.79
PhyloP100
0.26
PromoterAI
-0.051
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs375578873; hg19: chr17-4736884; API