chr6-63280206-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016571.3(LGSN):āc.1345C>Gā(p.Gln449Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00016 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_016571.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGSN | NM_016571.3 | c.1345C>G | p.Gln449Glu | missense_variant | 4/4 | ENST00000370657.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGSN | ENST00000370657.9 | c.1345C>G | p.Gln449Glu | missense_variant | 4/4 | 1 | NM_016571.3 | P1 | |
LGSN | ENST00000370658.9 | c.*297C>G | 3_prime_UTR_variant | 5/5 | 1 | ||||
LGSN | ENST00000622415.1 | c.*1070C>G | 3_prime_UTR_variant | 5/5 | 2 | ||||
LGSN | ENST00000485906.6 | c.530-779C>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000195 AC: 49AN: 251410Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135874
GnomAD4 exome AF: 0.000163 AC: 238AN: 1461858Hom.: 0 Cov.: 33 AF XY: 0.000180 AC XY: 131AN XY: 727232
GnomAD4 genome AF: 0.000138 AC: 21AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.1345C>G (p.Q449E) alteration is located in exon 4 (coding exon 4) of the LGSN gene. This alteration results from a C to G substitution at nucleotide position 1345, causing the glutamine (Q) at amino acid position 449 to be replaced by a glutamic acid (E). 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