19-54462400-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001301782.2(LENG9):c.1127G>A(p.Ser376Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,612,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/15 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.1127G>A | p.Ser376Asn | 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.1127G>A | p.Ser376Asn | missense_variant | Exon 1 of 1 | 6 | NM_001301782.2 | ENSP00000479355.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152256Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460742Hom.: 0 Cov.: 69 AF XY: 0.00000963 AC XY: 7AN XY: 726588
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1196G>A (p.S399N) 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 1196, causing the serine (S) at amino acid position 399 to be replaced by an asparagine (N). 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