rs9640055

Variant names:

• chr7-7989885-A-G
• rs9640055
• NM_138426.4:c.458-14023A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138426.4(GLCCI1):​c.458-14023A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0826 in 152,168 control chromosomes in the GnomAD database, including 687 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 0.083 (687 hom., cov: 32)
• Consequence: GLCCI1 NM_138426.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 3 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]

ENSG00000283549 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLCCI1	NM_138426.4	c.458-14023A>G		intron_variant	Intron 1 of 7	ENST00000223145.10	NP_612435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLCCI1	ENST00000223145.10	c.458-14023A>G		intron_variant	Intron 1 of 7	1	NM_138426.4	ENSP00000223145.5

Frequencies

GnomAD3 genomes AF: 0.0825 AC: 12539 AN: 152048 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0777

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

GnomAD4 genome AF: 0.0826 AC: 12565 AN: 152168 Hom.: 687 Cov.: 32 AF XY: 0.0861 AC XY: 6404 AN XY: 74400

African (AFR) AF: 0.132 AC: 5482 AN: 41534

American (AMR) AF: 0.123 AC: 1881 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3468

East Asian (EAS) AF: 0.188 AC: 975 AN: 5176

South Asian (SAS) AF: 0.0981 AC: 474 AN: 4832

European-Finnish (FIN) AF: 0.0720 AC: 764 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2609 AN: 67940

Other (OTH) AF: 0.0783 AC: 165 AN: 2108

Alfa AF: 0.0646 Hom.: 143

Bravo AF: 0.0885

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
DANN	Benign	0.63
PhyloP100		0.28
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: rs9640055; hg19: chr7-8029516;