chr9-4389941-G-C

Position:

• chr9-4389941-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.-151-41529C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,182 control chromosomes in the GnomAD database, including 4,455 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 (4455 hom., cov: 33)
• Consequence: GLIS3 XM_047422890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

Genes affected

GLIS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLIS3	XM_047422890.1	c.-151-41529C>G		intron_variant			XP_047278846.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34506 AN: 152064 Hom.: 4421 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.227 AC: 34591 AN: 152182 Hom.: 4455 Cov.: 33 AF XY: 0.230 AC XY: 17124 AN XY: 74398

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.232

Alfa AF: 0.203 Hom.: 411

Bravo AF: 0.235

Asia WGS AF: 0.345 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3933331; hg19: chr9-4389941;