9-4482706-T-C

Position:

• chr9-4482706-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+6922A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,160 control chromosomes in the GnomAD database, including 34,725 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 0.66 (34725 hom., cov: 33)
• Consequence: GLIS3 XM_047422890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

Genes affected

GLIS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLIS3	XM_047422890.1	c.-152+6922A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100837 AN: 152042 Hom.: 34680 Cov.: 33

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.663 AC: 100939 AN: 152160 Hom.: 34725 Cov.: 33 AF XY: 0.665 AC XY: 49477 AN XY: 74368

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.661

Alfa AF: 0.574 Hom.: 32378

Bravo AF: 0.677

Asia WGS AF: 0.707 AC: 2457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491734; hg19: chr9-4482706;