4-53535732-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001126328.3(LNX1):c.381-27505G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 152,236 control chromosomes in the GnomAD database, including 583 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association not found (★).
Frequency
Consequence
NM_001126328.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LNX1 | NM_001126328.3 | c.381-27505G>A | intron_variant | Intron 2 of 10 | ENST00000263925.8 | NP_001119800.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LNX1 | ENST00000263925.8 | c.381-27505G>A | intron_variant | Intron 2 of 10 | 1 | NM_001126328.3 | ENSP00000263925.7 | |||
ENSG00000282278 | ENST00000507166.5 | c.1017+109767C>T | intron_variant | Intron 12 of 23 | 2 | ENSP00000423325.1 |
Frequencies
GnomAD3 genomes AF: 0.0888 AC: 13507AN: 152118Hom.: 580 Cov.: 32
GnomAD4 genome AF: 0.0888 AC: 13524AN: 152236Hom.: 583 Cov.: 32 AF XY: 0.0857 AC XY: 6380AN XY: 74432
ClinVar
Submissions by phenotype
Lip and oral cavity carcinoma Other:1
No significant association was observed between SNP rs1435218 with oral cancer. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at