chrX-153875809-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001278116.2(L1CAM):c.28C>G(p.Pro10Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000912 in 1,096,743 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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. P10S) has been classified as Benign.
Frequency
Consequence
NM_001278116.2 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 |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.28C>G | p.Pro10Ala | missense_variant | 2/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.28C>G | p.Pro10Ala | missense_variant | 1/28 | ||
L1CAM | NM_024003.3 | c.28C>G | p.Pro10Ala | missense_variant | 1/27 | ||
L1CAM | NM_001143963.2 | c.28C>G | p.Pro10Ala | missense_variant | 1/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.28C>G | p.Pro10Ala | missense_variant | 2/29 | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome AF: 9.12e-7 AC: 1AN: 1096743Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 362463
GnomAD4 genome ? Cov.: 23
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at