rs12082358

Variant names:

• chr1-53690951-A-C
• rs12082358
• NM_001367484.1:c.259+46855T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-53690951-A-C
• chr1-53690951-A-G
• chr1-53690951-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367484.1(GLIS1):​c.259+46855T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,142 control chromosomes in the GnomAD database, including 3,992 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 (3992 hom., cov: 32)
• Consequence: GLIS1 NM_001367484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLIS1	NM_001367484.1	c.259+46855T>G		intron_variant	Intron 2 of 10	ENST00000628545.2	NP_001354413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLIS1	ENST00000628545.2	c.259+46855T>G		intron_variant	Intron 2 of 10	5	NM_001367484.1	ENSP00000486112.1
GLIS1	ENST00000312233.4	c.-267+42953T>G		intron_variant	Intron 1 of 9	2		ENSP00000309653.2

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34372 AN: 152024 Hom.: 3988 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.226 AC: 34398 AN: 152142 Hom.: 3992 Cov.: 32 AF XY: 0.221 AC XY: 16444 AN XY: 74388

African (AFR) AF: 0.264 AC: 10952 AN: 41514

American (AMR) AF: 0.207 AC: 3171 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3472

East Asian (EAS) AF: 0.297 AC: 1537 AN: 5172

South Asian (SAS) AF: 0.128 AC: 615 AN: 4802

European-Finnish (FIN) AF: 0.173 AC: 1837 AN: 10594

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14796 AN: 67970

Other (OTH) AF: 0.236 AC: 498 AN: 2112

Alfa AF: 0.199 Hom.: 2174

Bravo AF: 0.235

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.55
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12082358; hg19: chr1-54156624;