Variant chr14-96385734-T-C 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.*50T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 1,450,678 control chromosomes in the GnomAD database, including 128,162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 10029 hom., cov: 32)

Exomes 𝑓: 0.42 ( 118133 hom. )

Consequence

GSKIP
NM_016472.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.354

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=-0.79).

BP6

Variant 14-96385734-T-C is Benign according to our data. Variant chr14-96385734-T-C is described in ClinVar as [Benign]. Clinvar id is 1225936.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
GSKIP	NM_016472.5 linkuse as main transcript	c.*50T>C	3_prime_UTR_variant	4/4	ENST00000555181.6
GSKIP	NM_001271904.1 linkuse as main transcript	c.*50T>C	3_prime_UTR_variant	4/4
GSKIP	NM_001271905.2 linkuse as main transcript	c.*50T>C	3_prime_UTR_variant	4/4
GSKIP	NM_001271906.2 linkuse as main transcript	c.*50T>C	3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
GSKIP	ENST00000555181.6 linkuse as main transcript	c.*50T>C	3_prime_UTR_variant	4/4	1	NM_016472.5	P1
GSKIP	ENST00000438650.5 linkuse as main transcript	c.*50T>C	3_prime_UTR_variant	3/3	2		P1
GSKIP	ENST00000554182.5 linkuse as main transcript	c.*50T>C	3_prime_UTR_variant	4/4	2		P1
GSKIP	ENST00000556095.5 linkuse as main transcript	c.*50T>C	3_prime_UTR_variant	4/4	2		P1

Frequencies

GnomAD3 genomes

AF:

0.339

AC:

51566

AN:

151976

Hom.:

10030

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.403

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.248

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.439

Gnomad OTH

AF:

0.323

GnomAD3 exomes

AF:

0.377

AC:

74411

AN:

197448

Hom.:

15211

AF XY:

0.376

AC XY:

40949

AN XY:

108924

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.450

Gnomad ASJ exome

AF:

0.340

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.251

Gnomad FIN exome

AF:

0.418

Gnomad NFE exome

AF:

0.444

Gnomad OTH exome

AF:

0.365

GnomAD4 exome

AF:

0.418

AC:

542420

AN:

1298584

Hom.:

118133

Cov.:

AF XY:

0.414

AC XY:

268523

AN XY:

649292

show subpopulations

Gnomad4 AFR exome

AF:

0.147

Gnomad4 AMR exome

AF:

0.439

Gnomad4 ASJ exome

AF:

0.338

Gnomad4 EAS exome

AF:

0.193

Gnomad4 SAS exome

AF:

0.258

Gnomad4 FIN exome

AF:

0.417

Gnomad4 NFE exome

AF:

0.449

Gnomad4 OTH exome

AF:

0.374

GnomAD4 genome

AF:

0.339

AC:

51575

AN:

152094

Hom.:

10029

Cov.:

AF XY:

0.337

AC XY:

25032

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.403

Gnomad4 ASJ

AF:

0.324

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.249

Gnomad4 FIN

AF:

0.408

Gnomad4 NFE

AF:

0.439

Gnomad4 OTH

AF:

0.320

Alfa

AF:

0.403

Hom.:

13506

Bravo

AF:

0.333

Asia WGS

AF:

0.208

AC:

723

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

-0.79

CADD

Benign

5.7

DANN

Benign

0.77

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