19-54462272-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001301782.2(LENG9):c.1255G>A(p.Gly419Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,608,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001301782.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LENG9 | NM_001301782.2 | c.1255G>A | p.Gly419Arg | missense_variant | Exon 1 of 1 | ENST00000611161.2 | NP_001288711.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LENG9 | ENST00000611161.2 | c.1255G>A | p.Gly419Arg | missense_variant | Exon 1 of 1 | 6 | NM_001301782.2 | ENSP00000479355.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000244 AC: 6AN: 245652Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 132642
GnomAD4 exome AF: 0.00000755 AC: 11AN: 1456076Hom.: 0 Cov.: 68 AF XY: 0.00000414 AC XY: 3AN XY: 723868
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1324G>A (p.G442R) alteration is located in exon 1 (coding exon 1) of the LENG9 gene. This alteration results from a G to A substitution at nucleotide position 1324, causing the glycine (G) at amino acid position 442 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at