Genetic Variant GLCCI1:p.Gly44Cys (chr7-7969480-G-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_138426.4(GLCCI1):c.130G>T(p.Gly44Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G44S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GLCCI1
NM_138426.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17

Publications

0 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.25208116).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138426.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLCCI1	NM_138426.4	MANE Select	c.130G>T	p.Gly44Cys	missense	Exon 1 of 8	NP_612435.1	Q86VQ1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GLCCI1	ENST00000223145.10	TSL:1 MANE Select	c.130G>T	p.Gly44Cys	missense	Exon 1 of 8	ENSP00000223145.5	Q86VQ1
GLCCI1	ENST00000865612.1		c.130G>T	p.Gly44Cys	missense	Exon 1 of 8	ENSP00000535671.1
GLCCI1	ENST00000924964.1		c.130G>T	p.Gly44Cys	missense	Exon 1 of 8	ENSP00000595023.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

866588

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

404894

African (AFR)

AF:

0.00

AC:

AN:

16338

American (AMR)

AF:

0.00

AC:

AN:

2244

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6340

East Asian (EAS)

AF:

0.00

AC:

AN:

6298

South Asian (SAS)

AF:

0.00

AC:

AN:

17542

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4792

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1820

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

781776

Other (OTH)

AF:

0.00

AC:

AN:

29438

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.076

BayesDel_noAF

Benign

-0.35

CADD

Benign

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.012

Eigen

Benign

-0.18

Eigen_PC

Benign

-0.30

FATHMM_MKL

Benign

0.43

LIST_S2

Benign

0.35

M_CAP

Benign

0.024

MetaRNN

Benign

0.25

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.55

PhyloP100

1.2

PrimateAI

Pathogenic

0.90

PROVEAN

Benign

-0.39

REVEL

Benign

0.22

Sift

Benign

0.039

Sift4G

Benign

0.076

Polyphen

1.0

Vest4

0.29

MutPred

0.27

Loss of relative solvent accessibility (P = 0.0186)

MVP

0.42

MPC

0.98

ClinPred

0.78

GERP RS

1.2

PromoterAI

-0.0037

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

Varity_R

0.10

gMVP

0.26

Mutation Taster

=96/4

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over