Variant 14-96363513-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000438650.5(GSKIP):c.-57G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,724 control chromosomes in the GnomAD database, including 9,897 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 9863 hom., cov: 29)

Exomes 𝑓: 0.19 ( 34 hom. )

Consequence

GSKIP
ENST00000438650.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.692

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=-0.73).

BP6

Variant 14-96363513-G-T is Benign according to our data. Variant chr14-96363513-G-T is described in ClinVar as [Benign]. Clinvar id is 1273638.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	Effect	MANE
GSKIP	NM_016472.5 linkuse as main transcript	upstream_gene_variant	ENST00000555181.6
GSKIP	NM_001271905.2 linkuse as main transcript	upstream_gene_variant
GSKIP	NM_001271906.2 linkuse as main transcript	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSKIP	ENST00000555181.6 linkuse as main transcript			upstream_gene_variant		1	NM_016472.5	P1

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

50756

AN:

150700

Hom.:

9864

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.323

Gnomad EAS

AF:

0.193

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.320

GnomAD4 exome

AF:

0.190

AC:

173

AN:

912

Hom.:

Cov.:

AF XY:

0.190

AC XY:

114

AN XY:

600

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0833

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.227

Gnomad4 NFE exome

AF:

0.234

Gnomad4 OTH exome

AF:

0.308

GnomAD4 genome

AF:

0.337

AC:

50766

AN:

150812

Hom.:

9863

Cov.:

AF XY:

0.334

AC XY:

24605

AN XY:

73682

show subpopulations

Gnomad4 AFR

AF:

0.162

Gnomad4 AMR

AF:

0.402

Gnomad4 ASJ

AF:

0.323

Gnomad4 EAS

AF:

0.193

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.407

Gnomad4 NFE

AF:

0.437

Gnomad4 OTH

AF:

0.316

Alfa

AF:

0.236

Hom.:

630

Bravo

AF:

0.333

Asia WGS

AF:

0.203

AC:

701

AN:

3456

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 25, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Benign

0.88

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

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