rs4740788

chr9-4481668-T-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+7960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,096 control chromosomes in the GnomAD database, including 2,318 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 0.16 (2318 hom., cov: 32)
• Consequence: GLIS3 XM_047422890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86

Genes affected

GLIS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLIS3	XM_047422890.1	c.-152+7960A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24633 AN: 151978 Hom.: 2314 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.162 AC: 24660 AN: 152096 Hom.: 2318 Cov.: 32 AF XY: 0.161 AC XY: 11961 AN XY: 74348

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0760

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.151

Alfa AF: 0.134 Hom.: 2075

Bravo AF: 0.173

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.8
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4740788; hg19: chr9-4481668;