Variant chr7-7969649-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_138426.4(GLCCI1):c.299C>T(p.Ala100Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00502 in 1,012,632 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 3 hom., cov: 31)

Exomes 𝑓: 0.0052 ( 11 hom. )

Consequence

GLCCI1
NM_138426.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.191

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0012222826).

BP6

Variant 7-7969649-C-T is Benign according to our data. Variant chr7-7969649-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2657321.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLCCI1	NM_138426.4 linkuse as main transcript	c.299C>T	p.Ala100Val	missense_variant	1/8	ENST00000223145.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
GLCCI1	ENST00000223145.10 linkuse as main transcript	c.299C>T	p.Ala100Val	missense_variant	1/8	1	NM_138426.4	P1
GLCCI1-DT	ENST00000428660.1 linkuse as main transcript	n.132+123G>A		intron_variant, non_coding_transcript_variant		4
GLCCI1	ENST00000414914.5 linkuse as main transcript			upstream_gene_variant		3
GLCCI1	ENST00000430798.1 linkuse as main transcript			upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00418

AC:

613

AN:

146528

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00139

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00373

Gnomad ASJ

AF:

0.00354

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00911

Gnomad FIN

AF:

0.00332

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00619

Gnomad OTH

AF:

0.00445

GnomAD3 exomes

AF:

0.0106

AC:

AN:

282

Hom.:

AF XY:

0.0123

AC XY:

AN XY:

162

show subpopulations

Gnomad SAS exome

AF:

0.500

Gnomad NFE exome

AF:

0.00730

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00517

AC:

4473

AN:

865998

Hom.:

Cov.:

AF XY:

0.00521

AC XY:

2127

AN XY:

408270

show subpopulations

Gnomad4 AFR exome

AF:

0.000555

Gnomad4 AMR exome

AF:

0.00268

Gnomad4 ASJ exome

AF:

0.00347

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00640

Gnomad4 FIN exome

AF:

0.00162

Gnomad4 NFE exome

AF:

0.00525

Gnomad4 OTH exome

AF:

0.00567

GnomAD4 genome

AF:

0.00419

AC:

614

AN:

146634

Hom.:

Cov.:

AF XY:

0.00388

AC XY:

277

AN XY:

71378

show subpopulations

Gnomad4 AFR

AF:

0.00139

Gnomad4 AMR

AF:

0.00372

Gnomad4 ASJ

AF:

0.00354

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00933

Gnomad4 FIN

AF:

0.00332

Gnomad4 NFE

AF:

0.00619

Gnomad4 OTH

AF:

0.00440

Alfa

AF:

0.00355

Hom.:

Bravo

AF:

0.00420

ExAC

AF:

0.00411

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2022

GLCCI1: BP2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.028

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.65

FATHMM_MKL

Benign

0.014

LIST_S2

Benign

0.50

M_CAP

Benign

0.069

MetaRNN

Benign

0.0012

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.55

MutationTaster

Benign

1.0

PrimateAI

Pathogenic

0.87

PROVEAN

Benign

-1.0

REVEL

Benign

0.029

Sift

Benign

0.098

Sift4G

Benign

0.12

Polyphen

0.13

Vest4

0.070

MPC

0.70

ClinPred

0.10

GERP RS

0.63

Varity_R

0.041

gMVP

0.36

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