chr6-63280818-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016571.3(LGSN):c.733G>A(p.Asp245Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,842 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 (★).
Frequency
Consequence
NM_016571.3 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 | UniProt |
---|---|---|---|---|---|---|---|
LGSN | NM_016571.3 | c.733G>A | p.Asp245Asn | missense_variant | 4/4 | ENST00000370657.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGSN | ENST00000370657.9 | c.733G>A | p.Asp245Asn | missense_variant | 4/4 | 1 | NM_016571.3 | P1 | |
LGSN | ENST00000370658.9 | c.529+204G>A | intron_variant | 1 | |||||
LGSN | ENST00000622415.1 | c.*458G>A | 3_prime_UTR_variant | 5/5 | 2 | ||||
LGSN | ENST00000485906.6 | c.529+204G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251040Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135740
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461730Hom.: 0 Cov.: 33 AF XY: 0.0000275 AC XY: 20AN XY: 727160
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.733G>A (p.D245N) alteration is located in exon 4 (coding exon 4) of the LGSN gene. This alteration results from a G to A substitution at nucleotide position 733, causing the aspartic acid (D) at amino acid position 245 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