5-177332142-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006816.3(LMAN2):c.1015G>C(p.Val339Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,370 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006816.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMAN2 | NM_006816.3 | c.1015G>C | p.Val339Leu | missense_variant | Exon 8 of 8 | ENST00000303127.12 | NP_006807.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249540Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135458
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461370Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727010
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1015G>C (p.V339L) alteration is located in exon 8 (coding exon 8) of the LMAN2 gene. This alteration results from a G to C substitution at nucleotide position 1015, causing the valine (V) at amino acid position 339 to be replaced by a leucine (L). 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