rs398123053
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM5PP3
The NM_012106.4(ARL2BP):āc.134T>Cā(p.Met45Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. M45R) has been classified as Uncertain significance.
Frequency
Consequence
NM_012106.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARL2BP | NM_012106.4 | c.134T>C | p.Met45Thr | missense_variant | 3/6 | ENST00000219204.8 | |
LOC124903697 | XR_007065082.1 | n.1491A>G | non_coding_transcript_exon_variant | 2/2 | |||
ARL2BP | XM_047433883.1 | c.38T>C | p.Met13Thr | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARL2BP | ENST00000219204.8 | c.134T>C | p.Met45Thr | missense_variant | 3/6 | 1 | NM_012106.4 | P1 | |
ARL2BP | ENST00000563234.1 | c.128T>C | p.Met43Thr | missense_variant | 3/6 | 2 | |||
ARL2BP | ENST00000562023.5 | c.101-1210T>C | intron_variant | 3 | |||||
PLLP | ENST00000564376.1 | n.377A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at