rs797906

Variant names:

• chr1-53725022-C-A
• rs797906
• NM_001367484.1:c.259+12784G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-53725022-C-A
• chr1-53725022-C-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+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
• Publications: 12 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=-0.93).
• 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 rank	MANE	Protein	UniProt
GLIS1	NM_001367484.1	c.259+12784G>T		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+12784G>T		intron_variant	Intron 2 of 10	5	NM_001367484.1	ENSP00000486112.1
GLIS1	ENST00000312233.4	c.-267+8882G>T		intron_variant	Intron 1 of 9	2		ENSP00000309653.2

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

African (AFR) AF: 0.520 AC: 21508 AN: 41382

American (AMR) AF: 0.389 AC: 5943 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2582 AN: 5158

South Asian (SAS) AF: 0.313 AC: 1504 AN: 4806

European-Finnish (FIN) AF: 0.321 AC: 3383 AN: 10546

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.353 AC: 23962 AN: 67940

Other (OTH) AF: 0.397 AC: 837 AN: 2108

Alfa AF: 0.372 Hom.: 34150

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
PhyloP100		0.065
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: rs797906; hg19: chr1-54190695;