7-42026191-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000168.6(GLI3):c.1242+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 1,605,350 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000168.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLI3 | NM_000168.6 | c.1242+8G>A | splice_region_variant, intron_variant | ENST00000395925.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLI3 | ENST00000395925.8 | c.1242+8G>A | splice_region_variant, intron_variant | 5 | NM_000168.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152216Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000561 AC: 136AN: 242542Hom.: 2 AF XY: 0.000473 AC XY: 62AN XY: 131116
GnomAD4 exome AF: 0.000129 AC: 187AN: 1453020Hom.: 1 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 722776
GnomAD4 genome AF: 0.000381 AC: 58AN: 152330Hom.: 1 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74488
ClinVar
Submissions by phenotype
Pallister-Hall syndrome;C0265306:Greig cephalopolysyndactyly syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 11, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 08, 2020 | - - |
Pallister-Hall syndrome;C0265306:Greig cephalopolysyndactyly syndrome;C1868111:Polysyndactyly 4;C4282400:Polydactyly, postaxial, type A1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 11, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at