Variant 1-47250368-TAA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001048166.1(STIL):c.*766_*767del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 173,964 control chromosomes in the GnomAD database, including 18,447 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.42 ( 15821 hom., cov: 0)

Exomes 𝑓: 0.48 ( 2626 hom. )

Consequence

STIL
NM_001048166.1 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.61

Variant links:

Genes affected

STIL (HGNC:10879): (STIL centriolar assembly protein) This gene encodes a cytoplasmic protein implicated in regulation of the mitotic spindle checkpoint, a regulatory pathway that monitors chromosome segregation during cell division to ensure the proper distribution of chromosomes to daughter cells. The protein is phosphorylated in mitosis and in response to activation of the spindle checkpoint, and disappears when cells transition to G1 phase. It interacts with a mitotic regulator, and its expression is required to efficiently activate the spindle checkpoint. It is proposed to regulate Cdc2 kinase activity during spindle checkpoint arrest. Chromosomal deletions that fuse this gene and the adjacent locus commonly occur in T cell leukemias, and are thought to arise through illegitimate V-(D)-J recombination events. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

STIL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-47250368-TAA-T is Benign according to our data. Variant chr1-47250368-TAA-T is described in ClinVar as [Benign]. Clinvar id is 297544.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STIL	NM_001048166.1 linkuse as main transcript	c.766_767del		3_prime_UTR_variant	17/17	ENST00000371877.8	NP_001041631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STIL	ENST00000371877.8 linkuse as main transcript	c.766_767del		3_prime_UTR_variant	17/17	1	NM_001048166.1	ENSP00000360944	P5	Q15468-2

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64521

AN:

151854

Hom.:

15808

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.466

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.656

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.643

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.460

GnomAD4 exome

AF:

0.477

AC:

10487

AN:

21990

Hom.:

2626

AF XY:

0.481

AC XY:

4851

AN XY:

10082

show subpopulations

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

0.409

Gnomad4 ASJ exome

AF:

0.634

Gnomad4 EAS exome

AF:

0.387

Gnomad4 SAS exome

AF:

0.474

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.515

Gnomad4 OTH exome

AF:

0.476

GnomAD4 genome

AF:

0.425

AC:

64559

AN:

151974

Hom.:

15821

Cov.:

AF XY:

0.431

AC XY:

31994

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.656

Gnomad4 EAS

AF:

0.448

Gnomad4 SAS

AF:

0.551

Gnomad4 FIN

AF:

0.643

Gnomad4 NFE

AF:

0.521

Gnomad4 OTH

AF:

0.463

Alfa

AF:

0.480

Hom.:

2330

Bravo

AF:

0.396

Asia WGS

AF:

0.492

AC:

1705

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Primary Microcephaly, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over