NM_138426.4:c.814-1586G>A

Variant names:

• chr7-8058510-G-A
• rs9648623
• NM_138426.4:c.814-1586G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

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.814-1586G>A		intron	N/A	NP_612435.1	Q86VQ1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLCCI1	ENST00000223145.10	TSL:1 MANE Select	c.814-1586G>A		intron	N/A	ENSP00000223145.5	Q86VQ1
	GLCCI1	ENST00000865612.1		c.811-1586G>A		intron	N/A	ENSP00000535671.1
	GLCCI1	ENST00000924964.1		c.814-1586G>A		intron	N/A	ENSP00000595023.1

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

African (AFR) AF: 0.281 AC: 11665 AN: 41466

American (AMR) AF: 0.135 AC: 2070 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3460

East Asian (EAS) AF: 0.0172 AC: 89 AN: 5186

South Asian (SAS) AF: 0.134 AC: 647 AN: 4820

European-Finnish (FIN) AF: 0.178 AC: 1877 AN: 10568

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12771 AN: 67972

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.181 Hom.: 4517

Bravo AF: 0.199

Asia WGS AF: 0.0850 AC: 295 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9648623; hg19: chr7-8098140;