7-41961326-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000168.6(GLI3):c.*3004G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,342 control chromosomes in the GnomAD database, including 7,217 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_000168.6 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLI3 | ENST00000395925 | c.*3004G>A | 3_prime_UTR_variant | Exon 15 of 15 | 5 | NM_000168.6 | ENSP00000379258.3 | |||
GLI3 | ENST00000677605 | c.*3004G>A | 3_prime_UTR_variant | Exon 15 of 15 | ENSP00000503743.1 | |||||
GLI3 | ENST00000678429 | c.*3004G>A | 3_prime_UTR_variant | Exon 15 of 15 | ENSP00000502957.1 | |||||
GLI3 | ENST00000677288 | c.*3004G>A | 3_prime_UTR_variant | Exon 14 of 14 | ENSP00000503986.1 |
Frequencies
GnomAD3 genomes AF: 0.278 AC: 42207AN: 151894Hom.: 7194 Cov.: 33
GnomAD4 exome AF: 0.342 AC: 113AN: 330Hom.: 17 Cov.: 0 AF XY: 0.328 AC XY: 67AN XY: 204
GnomAD4 genome AF: 0.278 AC: 42237AN: 152012Hom.: 7200 Cov.: 33 AF XY: 0.282 AC XY: 20917AN XY: 74286
ClinVar
Submissions by phenotype
Greig cephalopolysyndactyly syndrome Benign:1
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
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
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at