NM_138426.4:c.458-14405T>C

Variant names:

• chr7-7989503-T-C
• rs37995
• NM_138426.4:c.458-14405T>C

Variant summary

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

The NM_138426.4(GLCCI1):​c.458-14405T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,954 control chromosomes in the GnomAD database, including 14,245 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 0.43 (14245 hom., cov: 32)
• Consequence: GLCCI1 NM_138426.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20
• Publications: 2 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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLCCI1	NM_138426.4	c.458-14405T>C		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.458-14405T>C		intron_variant	Intron 1 of 7	1	NM_138426.4	ENSP00000223145.5

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65244 AN: 151836 Hom.: 14244 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.429 AC: 65241 AN: 151954 Hom.: 14245 Cov.: 32 AF XY: 0.424 AC XY: 31492 AN XY: 74300

African (AFR) AF: 0.422 AC: 17500 AN: 41498

American (AMR) AF: 0.380 AC: 5803 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3468

East Asian (EAS) AF: 0.264 AC: 1369 AN: 5176

South Asian (SAS) AF: 0.318 AC: 1532 AN: 4818

European-Finnish (FIN) AF: 0.416 AC: 4398 AN: 10564

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31249 AN: 67842

Other (OTH) AF: 0.443 AC: 936 AN: 2114

Alfa AF: 0.451 Hom.: 2604

Bravo AF: 0.430

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	16
DANN	Benign	0.91
PhyloP100		2.2
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: rs37995; hg19: chr7-8029134;