chr19-54462302-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001301782.2(LENG9):c.1225G>A(p.Ala409Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000363 in 1,602,258 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.1225G>A | p.Ala409Thr | 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.1225G>A | p.Ala409Thr | missense_variant | Exon 1 of 1 | 6 | NM_001301782.2 | ENSP00000479355.1 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000379 AC: 92AN: 243060Hom.: 0 AF XY: 0.000335 AC XY: 44AN XY: 131162
GnomAD4 exome AF: 0.000365 AC: 529AN: 1449888Hom.: 0 Cov.: 69 AF XY: 0.000338 AC XY: 243AN XY: 719660
GnomAD4 genome AF: 0.000341 AC: 52AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1294G>A (p.A432T) 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 1294, causing the alanine (A) at amino acid position 432 to be replaced by a threonine (T). 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