chr9-4411383-A-G

Position:

• chr9-4411383-A-G

Variant summary

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

The XM_047422890.1(GLIS3):​c.-151-62971T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,060 control chromosomes in the GnomAD database, including 28,081 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 0.60 (28081 hom., cov: 32)
• Consequence: GLIS3 XM_047422890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

GLIS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLIS3	XM_047422890.1	c.-151-62971T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90872 AN: 151942 Hom.: 28034 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.598 AC: 90978 AN: 152060 Hom.: 28081 Cov.: 32 AF XY: 0.597 AC XY: 44354 AN XY: 74322

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.604

Alfa AF: 0.528 Hom.: 30224

Bravo AF: 0.617

Asia WGS AF: 0.665 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7851353; hg19: chr9-4411383;