rs147579402
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_133642.5(LARGE1):c.788-29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00678 in 1,565,854 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_133642.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LARGE1 | NM_133642.5 | c.788-29A>G | intron_variant | ENST00000397394.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LARGE1 | ENST00000397394.8 | c.788-29A>G | intron_variant | 5 | NM_133642.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00546 AC: 830AN: 152108Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00590 AC: 1472AN: 249682Hom.: 9 AF XY: 0.00594 AC XY: 802AN XY: 134950
GnomAD4 exome AF: 0.00692 AC: 9784AN: 1413628Hom.: 41 Cov.: 24 AF XY: 0.00671 AC XY: 4738AN XY: 706342
GnomAD4 genome ? AF: 0.00545 AC: 830AN: 152226Hom.: 7 Cov.: 32 AF XY: 0.00547 AC XY: 407AN XY: 74434
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at