rs797906

chr1-53725022-C-Achr1-53725022-C-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+12784G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,878 control chromosomes in the GnomAD database, including 13,093 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 0.41 (13093 hom., cov: 31)
• Consequence: GLIS1 NM_001367484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLIS1	NM_001367484.1	c.259+12784G>T		intron_variant		ENST00000628545.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLIS1	ENST00000628545.2	c.259+12784G>T		intron_variant		5	NM_001367484.1	P2
GLIS1	ENST00000312233.4	c.-267+8882G>T		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61669 AN: 151760 Hom.: 13086 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.406 AC: 61715 AN: 151878 Hom.: 13093 Cov.: 31 AF XY: 0.404 AC XY: 29963 AN XY: 74216

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.397

Alfa AF: 0.362 Hom.: 20374

Bravo AF: 0.421

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.58
Dann	Benign	0.58

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: rs797906; hg19: chr1-54190695;