2-74497935-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001282430.2(LBX2):c.589G>A(p.Asp197Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000778 in 1,414,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D197H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001282430.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LBX2 | ENST00000377566.9 | c.589G>A | p.Asp197Asn | missense_variant | Exon 2 of 2 | 1 | NM_001282430.2 | ENSP00000366789.4 | ||
LBX2 | ENST00000460508.3 | c.577G>A | p.Asp193Asn | missense_variant | Exon 2 of 2 | 1 | ENSP00000417116.2 | |||
LBX2 | ENST00000550249.2 | n.883G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 | |||||
LBX2 | ENST00000341396 | c.*234G>A | 3_prime_UTR_variant | Exon 2 of 2 | 3 | ENSP00000450229.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000464 AC: 1AN: 215430Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 117364
GnomAD4 exome AF: 0.00000778 AC: 11AN: 1414500Hom.: 0 Cov.: 29 AF XY: 0.0000129 AC XY: 9AN XY: 698252
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at