rs28177

Positions:

• chr7-7977268-T-A
• chr7-7977268-T-C
• chr7-7977268-T-G

Variant summary

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

The NM_138426.4(GLCCI1):​c.457+7461T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,072 control chromosomes in the GnomAD database, including 43,237 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 0.75 (43237 hom., cov: 32)
• Consequence: GLCCI1 NM_138426.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLCCI1	NM_138426.4	c.457+7461T>A		intron_variant		ENST00000223145.10	NP_612435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLCCI1	ENST00000223145.10	c.457+7461T>A		intron_variant		1	NM_138426.4	ENSP00000223145	P1

Frequencies

GnomAD3 genomes AF: 0.750 AC: 114032 AN: 151952 Hom.: 43200 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.750 AC: 114119 AN: 152072 Hom.: 43237 Cov.: 32 AF XY: 0.749 AC XY: 55693 AN XY: 74334

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.755

Alfa AF: 0.626 Hom.: 1741

Bravo AF: 0.767

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.96
DANN	Benign	0.29

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: rs28177; hg19: chr7-8016899; COSMIC: COSV56205849; COSMIC: COSV56205849;