1-53712828-G-T

Position:

• chr1-53712828-G-T

Variant summary

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

The NM_001367484.1(GLIS1):​c.259+24978C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,988 control chromosomes in the GnomAD database, including 4,252 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 0.23 (4252 hom., cov: 31)
• Consequence: GLIS1 NM_001367484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLIS1	NM_001367484.1	c.259+24978C>A		intron_variant		ENST00000628545.2	NP_001354413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLIS1	ENST00000628545.2	c.259+24978C>A		intron_variant		5	NM_001367484.1	ENSP00000486112.1
GLIS1	ENST00000312233.4	c.-267+21076C>A		intron_variant		2		ENSP00000309653.2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35674 AN: 151870 Hom.: 4250 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.235 AC: 35697 AN: 151988 Hom.: 4252 Cov.: 31 AF XY: 0.230 AC XY: 17114 AN XY: 74292

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.244

Alfa AF: 0.150 Hom.: 346

Bravo AF: 0.244

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.53

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: rs12080993; hg19: chr1-54178501;