rs6476866

chr9-4459274-G-Achr9-4459274-G-C

Variant summary

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

The XM_047422890.1(GLIS3):c.-152+30354C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,908 control chromosomes in the GnomAD database, including 23,821 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 0.55 (23821 hom., cov: 31)
• Consequence: GLIS3 XM_047422890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

GLIS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLIS3	XM_047422890.1	c.-152+30354C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84150 AN: 151790 Hom.: 23801 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.554 AC: 84221 AN: 151908 Hom.: 23821 Cov.: 31 AF XY: 0.557 AC XY: 41328 AN XY: 74230

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.548

Alfa AF: 0.595 Hom.: 14388

Bravo AF: 0.545

Asia WGS AF: 0.617 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.040
Dann	Benign	0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6476866; hg19: chr9-4459274; COSMIC: COSV69444200;