rs9648623

chr7-8058510-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138426.4(GLCCI1):c.814-1586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,070 control chromosomes in the GnomAD database, including 3,329 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3329 hom., cov: 32)
• Consequence: GLCCI1 NM_138426.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLCCI1	NM_138426.4	c.814-1586G>A		intron_variant		ENST00000223145.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLCCI1	ENST00000223145.10	c.814-1586G>A		intron_variant		1	NM_138426.4	P1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30081 AN: 151952 Hom.: 3322 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.189

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.198 AC: 30082 AN: 152070 Hom.: 3329 Cov.: 32 AF XY: 0.195 AC XY: 14467 AN XY: 74338

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0172

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.187

Alfa AF: 0.178 Hom.: 3312

Bravo AF: 0.199

Asia WGS AF: 0.0850 AC: 295 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.5
Dann	Benign	0.75

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

Other links and lift over

dbSNP: rs9648623; hg19: chr7-8098140;