Variant 14-96382562-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_016472.5(GSKIP):c.258+57A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,341,172 control chromosomes in the GnomAD database, including 27,150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2316 hom., cov: 32)

Exomes 𝑓: 0.20 ( 24834 hom. )

Consequence

GSKIP
NM_016472.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.214

Variant links:

Genes affected

GSKIP (HGNC:20343): (GSK3B interacting protein) This gene encodes a protein that is involved as a negative regulator of GSK3-beta in the Wnt signaling pathway. The encoded protein may play a role in the retinoic acid signaling pathway by regulating the functional interactions between GSK3-beta, beta-catenin and cyclin D1, and it regulates the beta-catenin/N-cadherin pool. The encoded protein contains a GSK3-beta interacting domain (GID) in its C-terminus, which is similar to the GID of Axin. The protein also contains an evolutionarily conserved RII-binding domain, which facilitates binding with protein kinase-A and GSK3-beta, enabling its role as an A-kinase anchoring protein. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2012]

GSKIP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 14-96382562-A-G is Benign according to our data. Variant chr14-96382562-A-G is described in ClinVar as [Benign]. Clinvar id is 1238084.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
GSKIP	NM_016472.5 linkuse as main transcript	c.258+57A>G	intron_variant	ENST00000555181.6
GSKIP	NM_001271904.1 linkuse as main transcript	c.258+57A>G	intron_variant
GSKIP	NM_001271905.2 linkuse as main transcript	c.258+57A>G	intron_variant
GSKIP	NM_001271906.2 linkuse as main transcript	c.258+57A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSKIP	ENST00000555181.6 linkuse as main transcript	c.258+57A>G		intron_variant		1	NM_016472.5	P1

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23780

AN:

152040

Hom.:

2315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0462

Gnomad AMI

AF:

0.382

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.162

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.169

GnomAD4 exome

AF:

0.203

AC:

241699

AN:

1189014

Hom.:

24834

AF XY:

0.203

AC XY:

120442

AN XY:

593278

show subpopulations

Gnomad4 AFR exome

AF:

0.0411

Gnomad4 AMR exome

AF:

0.195

Gnomad4 ASJ exome

AF:

0.212

Gnomad4 EAS exome

AF:

0.207

Gnomad4 SAS exome

AF:

0.190

Gnomad4 FIN exome

AF:

0.162

Gnomad4 NFE exome

AF:

0.211

Gnomad4 OTH exome

AF:

0.198

GnomAD4 genome

AF:

0.156

AC:

23778

AN:

152158

Hom.:

2316

Cov.:

AF XY:

0.156

AC XY:

11629

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0460

Gnomad4 AMR

AF:

0.187

Gnomad4 ASJ

AF:

0.221

Gnomad4 EAS

AF:

0.181

Gnomad4 SAS

AF:

0.175

Gnomad4 FIN

AF:

0.162

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.176

Hom.:

334

Bravo

AF:

0.155

Asia WGS

AF:

0.162

AC:

564

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

8.9

DANN

Benign

0.69

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