Genetic Variant GLCCI1:p.Cys51Gly (chr7-7969501-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_138426.4(GLCCI1):c.151T>G(p.Cys51Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C51W) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000071 ( 0 hom., cov: 30)

Exomes 𝑓: 0.00062 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GLCCI1
NM_138426.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.182

Variant links:

Genes affected

GLCCI1 (HGNC:18713): (glucocorticoid induced 1) This gene encodes a protein of unknown function. Expression of this gene is induced by glucocorticoids and may be an early marker for glucocorticoid-induced apoptosis. Single nucleotide polymorphisms in this gene are associated with a decreased response to inhaled glucocorticoids in asthmatic patients. [provided by RefSeq, Feb 2012]

GLCCI1 links:

GLCCI1-DT (HGNC:40852): (GLCCI1 divergent transcript)

GLCCI1-DT links:

ENSG00000283549 (HGNC:):

ENSG00000283549 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.08105394).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLCCI1	NM_138426.4 link	c.151T>G	p.Cys51Gly	missense_variant	Exon 1 of 8	ENST00000223145.10	NP_612435.1	Q86VQ1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLCCI1	ENST00000223145.10 link	c.151T>G	p.Cys51Gly	missense_variant	Exon 1 of 8	1	NM_138426.4	ENSP00000223145.5		Q86VQ1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

141140

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000704

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000701

Gnomad SAS

AF:

0.000252

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000465

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000622

AC:

389

AN:

625488

Hom.:

Cov.:

AF XY:

0.000592

AC XY:

173

AN XY:

292416

show subpopulations

Gnomad4 AFR exome

AF:

0.000597

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.000468

Gnomad4 EAS exome

AF:

0.000853

Gnomad4 SAS exome

AF:

0.000389

Gnomad4 FIN exome

AF:

0.000472

Gnomad4 NFE exome

AF:

0.000633

Gnomad4 OTH exome

AF:

0.000520

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000708

AC:

AN:

141270

Hom.:

Cov.:

AF XY:

0.0000437

AC XY:

AN XY:

68688

show subpopulations

Gnomad4 AFR

AF:

0.0000755

Gnomad4 AMR

AF:

0.0000702

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000702

Gnomad4 SAS

AF:

0.000251

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000310

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Oct 12, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.151T>G (p.C51G) alteration is located in exon 1 (coding exon 1) of the GLCCI1 gene. This alteration results from a T to G substitution at nucleotide position 151, causing the cysteine (C) at amino acid position 51 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.040

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.54

DEOGEN2

Benign

0.025

Eigen

Benign

-0.98

Eigen_PC

Benign

-0.95

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.37

M_CAP

Benign

0.031

MetaRNN

Benign

0.081

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.34

PrimateAI

Pathogenic

0.88

PROVEAN

Benign

-1.2

REVEL

Benign

0.032

Sift

Benign

0.34

Sift4G

Benign

0.090

Polyphen

0.0

Vest4

0.24

MutPred

0.26

Gain of MoRF binding (P = 0.097);

MVP

0.20

MPC

0.59

ClinPred

0.042

GERP RS

0.57

Varity_R

0.070

gMVP

0.20

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