rs7851353

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33
Variant links:
Genes affected
GLIS3 (HGNC:28510): (GLIS family zinc finger 3) This gene is a member of the GLI-similar zinc finger protein family and encodes a nuclear protein with five C2H2-type zinc finger domains. This protein functions as both a repressor and activator of transcription and is specifically involved in the development of pancreatic beta cells, the thyroid, eye, liver and kidney. Mutations in this gene have been associated with neonatal diabetes and congenital hypothyroidism (NDH). Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only two have been determined. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 Protein UniProt
GLIS3XM_047422890.1 linkuse as main transcriptc.-151-62971T>C intron_variant XP_047278846.1
use as main transcriptn.4411383A>G intergenic_region

Ensembl

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

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7851353; hg19: chr9-4411383; API