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rs13101192

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005414.5(SKIL):c.1098+1535C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 150,642 control chromosomes in the GnomAD database, including 44,254 homozygotes. 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 0.76 ( 44254 hom., cov: 26)

Consequence

SKIL
NM_005414.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.175
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SKILNM_005414.5 linkuse as main transcriptc.1098+1535C>G intron_variant ENST00000259119.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SKILENST00000259119.9 linkuse as main transcriptc.1098+1535C>G intron_variant 1 NM_005414.5 P1P12757-1

Frequencies

GnomAD3 genomes
AF:
0.757
AC:
113878
AN:
150526
Hom.:
44246
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.556
Gnomad AMI
AF:
0.872
Gnomad AMR
AF:
0.813
Gnomad ASJ
AF:
0.826
Gnomad EAS
AF:
0.937
Gnomad SAS
AF:
0.715
Gnomad FIN
AF:
0.874
Gnomad MID
AF:
0.775
Gnomad NFE
AF:
0.831
Gnomad OTH
AF:
0.764
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.756
AC:
113917
AN:
150642
Hom.:
44254
Cov.:
26
AF XY:
0.758
AC XY:
55691
AN XY:
73474
show subpopulations
Gnomad4 AFR
AF:
0.555
Gnomad4 AMR
AF:
0.813
Gnomad4 ASJ
AF:
0.826
Gnomad4 EAS
AF:
0.937
Gnomad4 SAS
AF:
0.716
Gnomad4 FIN
AF:
0.874
Gnomad4 NFE
AF:
0.831
Gnomad4 OTH
AF:
0.761
Alfa
AF:
0.733
Hom.:
2430
Bravo
AF:
0.748
Asia WGS
AF:
0.768
AC:
2667
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
1.5
Dann
Benign
0.26

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13101192; hg19: chr3-170080752; API