rs7551844

Variant names:

• chr1-53595660-T-C
• rs7551844
• NM_001367484.1:c.438-670A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-53595660-T-C
• chr1-53595660-T-G

Variant summary

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

The NM_001367484.1(GLIS1):​c.438-670A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,160 control chromosomes in the GnomAD database, including 24,859 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 0.53 (24859 hom., cov: 33)
• Consequence: GLIS1 NM_001367484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLIS1	NM_001367484.1	c.438-670A>G		intron_variant	Intron 3 of 10	ENST00000628545.2	NP_001354413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLIS1	ENST00000628545.2	c.438-670A>G		intron_variant	Intron 3 of 10	5	NM_001367484.1	ENSP00000486112.1
GLIS1	ENST00000312233.4	c.-88-670A>G		intron_variant	Intron 2 of 9	2		ENSP00000309653.2

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81363 AN: 152040 Hom.: 24854 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.535 AC: 81377 AN: 152160 Hom.: 24859 Cov.: 33 AF XY: 0.541 AC XY: 40271 AN XY: 74384

African (AFR) AF: 0.228 AC: 9448 AN: 41504

American (AMR) AF: 0.693 AC: 10604 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1601 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2259 AN: 5172

South Asian (SAS) AF: 0.567 AC: 2734 AN: 4822

European-Finnish (FIN) AF: 0.739 AC: 7829 AN: 10592

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44884 AN: 67986

Other (OTH) AF: 0.580 AC: 1227 AN: 2114

Alfa AF: 0.621 Hom.: 18972

Bravo AF: 0.520

Asia WGS AF: 0.503 AC: 1750 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	2.2
DANN	Benign	0.51
PhyloP100		-1.9
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: rs7551844; hg19: chr1-54061333;