rs776980379

Variant names:

• chr7-7969363-T-A
• NM_138426.4:c.13T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-7969363-T-A
• chr7-7969363-T-C
• chr7-7969363-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_138426.4(GLCCI1):​c.13T>A​(p.Ser5Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000853 in 1,171,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S5A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 8.5e-7 (0 hom.)
• Consequence: GLCCI1 NM_138426.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

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]

GLCCI1-DT (HGNC:40852): (GLCCI1 divergent transcript)

ENSG00000283549 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08579263).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLCCI1	NM_138426.4	c.13T>A	p.Ser5Thr	missense_variant	Exon 1 of 8	ENST00000223145.10	NP_612435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLCCI1	ENST00000223145.10	c.13T>A	p.Ser5Thr	missense_variant	Exon 1 of 8	1	NM_138426.4	ENSP00000223145.5
GLCCI1-DT	ENST00000428660.1	n.132+409A>T		intron_variant	Intron 1 of 1	4
ENSG00000283549	ENST00000469183.5	n.492-34545T>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 8.53e-7 AC: 1 AN: 1171660 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 579276

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000106

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.095
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.92
DEOGEN2	Benign	0.012	T
Eigen	Benign	-0.69
Eigen_PC	Benign	-0.74
FATHMM_MKL	Benign	0.23	N
LIST_S2	Benign	0.29	T
M_CAP	Benign	0.0017	T
MetaRNN	Benign	0.086	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.81	L
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-0.19	N
REVEL	Benign	0.043
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.025	D
Polyphen		0.22	B
Vest4		0.18
MutPred		0.18		Gain of relative solvent accessibility (P = 0.0479);
MVP		0.29
MPC		0.40
ClinPred		0.31	T
Varity_R		0.46
gMVP		0.18

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-8008994;