rs6588480

chr1-53512446-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001367484.1(GLIS1):c.1883+2179T>C variant causes a intron change. The variant allele was found at a frequency of 0.773 in 152,106 control chromosomes in the GnomAD database, including 46,153 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 0.77 (46153 hom., cov: 32)
• Consequence: GLIS1 NM_001367484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.49

Genes affected

GLIS1 (HGNC:29525): (GLIS family zinc finger 1) GLIS1 is a GLI (MIM 165220)-related Kruppel-like zinc finger protein that functions as an activator and repressor of transcription (Kim et al., 2002 [PubMed 12042312]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLIS1	NM_001367484.1	c.1883+2179T>C		intron_variant		ENST00000628545.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLIS1	ENST00000628545.2	c.1883+2179T>C		intron_variant		5	NM_001367484.1	P2
GLIS1	ENST00000312233.4	c.1358+2179T>C		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117564 AN: 151988 Hom.: 46124 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.773 AC: 117639 AN: 152106 Hom.: 46153 Cov.: 32 AF XY: 0.771 AC XY: 57354 AN XY: 74350

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.803

Alfa AF: 0.826 Hom.: 111232

Bravo AF: 0.760

Asia WGS AF: 0.723 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
Cadd	Benign	20
Dann	Benign	0.83

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: rs6588480; hg19: chr1-53978119;