rs61758978

Variant names:

• chr7-41966238-C-G
• rs61758978
• NM_000168.6:c.2835G>C

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BS1 BS2

The NM_000168.6(GLI3):​c.2835G>C​(p.Leu945Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0252 in 1,608,778 control chromosomes in the GnomAD database, including 598 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.018 (41 hom., cov: 33)
  • Exomes 𝑓: 0.026 (557 hom.)
• Consequence: GLI3 NM_000168.6 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:11
• Conservation: PhyloP100: 0.498

Genes affected

GLI3 (HGNC:4319): (GLI family zinc finger 3) This gene encodes a protein which belongs to the C2H2-type zinc finger proteins subclass of the Gli family. They are characterized as DNA-binding transcription factors and are mediators of Sonic hedgehog (Shh) signaling. The protein encoded by this gene localizes in the cytoplasm and activates patched Drosophila homolog (PTCH) gene expression. It is also thought to play a role during embryogenesis. Mutations in this gene have been associated with several diseases, including Greig cephalopolysyndactyly syndrome, Pallister-Hall syndrome, preaxial polydactyly type IV, and postaxial polydactyly types A1 and B. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BP6: Variant 7-41966238-C-G is Benign according to our data. Variant chr7-41966238-C-G is described in ClinVar as [Benign]. Clinvar id is 194463.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-41966238-C-G is described in Lovd as [Benign]. Variant chr7-41966238-C-G is described in Lovd as [Likely_benign].
• BP7: Synonymous conserved (PhyloP=0.498 with no splicing effect.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0184 (2803/152310) while in subpopulation NFE AF= 0.0272 (1849/68010). AF 95% confidence interval is 0.0262. There are 41 homozygotes in gnomad4. There are 1272 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 2803 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLI3	NM_000168.6	c.2835G>C	p.Leu945Leu	synonymous_variant	Exon 15 of 15	ENST00000395925.8	NP_000159.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLI3	ENST00000395925.8	c.2835G>C	p.Leu945Leu	synonymous_variant	Exon 15 of 15	5	NM_000168.6	ENSP00000379258.3

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2802 AN: 152194 Hom.: 41 Cov.: 33

Gnomad AFR AF: 0.00533

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0175

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.0256

Gnomad NFE AF: 0.0272

Gnomad OTH AF: 0.0229

GnomAD3 exomes AF: 0.0195 AC: 4548 AN: 232916 Hom.: 74 AF XY: 0.0205 AC XY: 2629 AN XY: 128150

Gnomad AFR exome AF: 0.00423

Gnomad AMR exome AF: 0.0138

Gnomad ASJ exome AF: 0.0317

Gnomad EAS exome AF: 0.000113

Gnomad SAS exome AF: 0.0174

Gnomad FIN exome AF: 0.0178

Gnomad NFE exome AF: 0.0263

Gnomad OTH exome AF: 0.0252

GnomAD4 exome AF: 0.0259 AC: 37684 AN: 1456468 Hom.: 557 Cov.: 35 AF XY: 0.0257 AC XY: 18627 AN XY: 724822

Gnomad4 AFR exome AF: 0.00452

Gnomad4 AMR exome AF: 0.0149

Gnomad4 ASJ exome AF: 0.0311

Gnomad4 EAS exome AF: 0.000151

Gnomad4 SAS exome AF: 0.0167

Gnomad4 FIN exome AF: 0.0198

Gnomad4 NFE exome AF: 0.0288

Gnomad4 OTH exome AF: 0.0239

GnomAD4 genome AF: 0.0184 AC: 2803 AN: 152310 Hom.: 41 Cov.: 33 AF XY: 0.0171 AC XY: 1272 AN XY: 74472

Gnomad4 AFR AF: 0.00531

Gnomad4 AMR AF: 0.0174

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0130

Gnomad4 FIN AF: 0.0176

Gnomad4 NFE AF: 0.0272

Gnomad4 OTH AF: 0.0236

Alfa AF: 0.0241 Hom.: 21

Bravo AF: 0.0186

Asia WGS AF: 0.0100 AC: 35 AN: 3472

EpiCase AF: 0.0260

EpiControl AF: 0.0266

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:4

May 20, 2015

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided Benign:3

Nov 29, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Pallister-Hall syndrome;C0265306:Greig cephalopolysyndactyly syndrome Benign:1

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Greig cephalopolysyndactyly syndrome Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Polydactyly Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Pallister-Hall syndrome Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	8.1
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs61758978; hg19: chr7-42005836;