GeneBe

NM_005414.5:c.1099-6977delG

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_005414.5(SKIL):​c.1099-6977delG variant causes a intron 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 0.83 ( 52975 hom., cov: 0)

Consequence

SKIL
NM_005414.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

3 publications found
Variant links:
Genes affected
SKIL (HGNC:10897): (SKI like proto-oncogene) The protein encoded by this gene is a component of the SMAD pathway, which regulates cell growth and differentiation through transforming growth factor-beta (TGFB). In the absence of ligand, the encoded protein binds to the promoter region of TGFB-responsive genes and recruits a nuclear repressor complex. TGFB signaling causes SMAD3 to enter the nucleus and degrade this protein, allowing these genes to be activated. Four transcript variants encoding three different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SKILNM_005414.5 linkc.1099-6977delG intron_variant Intron 2 of 6 ENST00000259119.9 NP_005405.2 P12757-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SKILENST00000259119.9 linkc.1099-6978delG intron_variant Intron 2 of 6 1 NM_005414.5 ENSP00000259119.4 P12757-1

Frequencies

GnomAD3 genomes
AF:
0.833
AC:
126454
AN:
151868
Hom.:
52961
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.723
Gnomad AMI
AF:
0.874
Gnomad AMR
AF:
0.845
Gnomad ASJ
AF:
0.877
Gnomad EAS
AF:
0.942
Gnomad SAS
AF:
0.854
Gnomad FIN
AF:
0.918
Gnomad MID
AF:
0.823
Gnomad NFE
AF:
0.871
Gnomad OTH
AF:
0.827
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.832
AC:
126511
AN:
151988
Hom.:
52975
Cov.:
0
AF XY:
0.836
AC XY:
62074
AN XY:
74294
show subpopulations
African (AFR)
AF:
0.723
AC:
29919
AN:
41394
American (AMR)
AF:
0.845
AC:
12901
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.877
AC:
3038
AN:
3466
East Asian (EAS)
AF:
0.942
AC:
4879
AN:
5180
South Asian (SAS)
AF:
0.854
AC:
4122
AN:
4826
European-Finnish (FIN)
AF:
0.918
AC:
9695
AN:
10566
Middle Eastern (MID)
AF:
0.830
AC:
244
AN:
294
European-Non Finnish (NFE)
AF:
0.871
AC:
59180
AN:
67970
Other (OTH)
AF:
0.823
AC:
1736
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1051
2102
3153
4204
5255
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
884
1768
2652
3536
4420
<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:
0.843
Hom.:
6603
Bravo
AF:
0.824
Asia WGS
AF:
0.847
AC:
2937
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.0
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs11288195; hg19: chr3-170092053; API