chr4-53496255-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001126328.3(LNX1):c.1118A>G(p.Tyr373Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y373D) has been classified as Uncertain significance.
Frequency
Consequence
NM_001126328.3 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 |
---|---|---|---|---|---|---|---|
LNX1 | NM_001126328.3 | c.1118A>G | p.Tyr373Cys | missense_variant | 6/11 | ENST00000263925.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LNX1 | ENST00000263925.8 | c.1118A>G | p.Tyr373Cys | missense_variant | 6/11 | 1 | NM_001126328.3 | P1 | |
LNX1 | ENST00000306888.6 | c.830A>G | p.Tyr277Cys | missense_variant | 5/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251308Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135812
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461886Hom.: 0 Cov.: 34 AF XY: 0.0000165 AC XY: 12AN XY: 727244
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2023 | The c.1118A>G (p.Y373C) alteration is located in exon 6 (coding exon 5) of the LNX1 gene. This alteration results from a A to G substitution at nucleotide position 1118, causing the tyrosine (Y) at amino acid position 373 to be replaced by a cysteine (C). 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