18-46560210-CTCCTCCTCT-CTCCTCCTCTTCCTCCTCT
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_001384474.1(LOXHD1):c.2933_2934insAGAGGAGGA(p.Glu976_Glu978dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000129 in 1,551,784 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. E978E) has been classified as Likely benign.
Frequency
Consequence
NM_001384474.1 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.2933_2934insAGAGGAGGA | p.Glu976_Glu978dup | inframe_insertion | 19/41 | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.2933_2934insAGAGGAGGA | p.Glu976_Glu978dup | inframe_insertion | 19/41 | NM_001384474.1 | P1 | ||
LOXHD1 | ENST00000536736.5 | c.2933_2934insAGAGGAGGA | p.Glu976_Glu978dup | inframe_insertion | 19/40 | 5 | |||
LOXHD1 | ENST00000441551.6 | c.2599-2722_2599-2721insAGAGGAGGA | intron_variant | 5 | |||||
LOXHD1 | ENST00000335730.6 | n.2246_2247insAGAGGAGGA | non_coding_transcript_exon_variant | 12/27 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD4 exome AF: 7.14e-7 AC: 1AN: 1399604Hom.: 0 Cov.: 37 AF XY: 0.00000145 AC XY: 1AN XY: 690300
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at