18-11752923-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_182978.4(GNAL):c.447C>T(p.Pro149=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000448 in 1,585,622 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_182978.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAL | NM_182978.4 | c.447C>T | p.Pro149= | splice_region_variant, synonymous_variant | 2/12 | ENST00000334049.11 | |
GNAL | NM_001369387.1 | c.216C>T | p.Pro72= | splice_region_variant, synonymous_variant | 2/12 | ENST00000423027.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAL | ENST00000334049.11 | c.447C>T | p.Pro149= | splice_region_variant, synonymous_variant | 2/12 | 1 | NM_182978.4 | ||
GNAL | ENST00000423027.8 | c.216C>T | p.Pro72= | splice_region_variant, synonymous_variant | 2/12 | 1 | NM_001369387.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000879 AC: 22AN: 250408Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135408
GnomAD4 exome AF: 0.0000467 AC: 67AN: 1433476Hom.: 0 Cov.: 26 AF XY: 0.0000475 AC XY: 34AN XY: 715154
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74318
ClinVar
Submissions by phenotype
Dystonic disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at