6-63280853-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000370657.9(LGSN):āc.698A>Gā(p.Asn233Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,613,870 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
ENST00000370657.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LGSN | NM_016571.3 | c.698A>G | p.Asn233Ser | missense_variant | 4/4 | ENST00000370657.9 | NP_057655.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LGSN | ENST00000370657.9 | c.698A>G | p.Asn233Ser | missense_variant | 4/4 | 1 | NM_016571.3 | ENSP00000359691 | P1 | |
LGSN | ENST00000370658.9 | c.529+169A>G | intron_variant | 1 | ENSP00000359692 | |||||
LGSN | ENST00000622415.1 | c.*423A>G | 3_prime_UTR_variant | 5/5 | 2 | ENSP00000479173 | ||||
LGSN | ENST00000485906.6 | c.529+169A>G | intron_variant | 3 | ENSP00000431246 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250584Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135566
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461692Hom.: 0 Cov.: 33 AF XY: 0.0000536 AC XY: 39AN XY: 727158
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2022 | The c.698A>G (p.N233S) alteration is located in exon 4 (coding exon 4) of the LGSN gene. This alteration results from a A to G substitution at nucleotide position 698, causing the asparagine (N) at amino acid position 233 to be replaced by a serine (S). 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