rs1555941129
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 9P and 4B. PVS1PP5BS2
The NM_004312.3(ARR3):c.298C>T(p.Arg100Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000638 in 1,098,025 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004312.3 stop_gained
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 |
---|---|---|---|---|---|---|---|
ARR3 | NM_004312.3 | c.298C>T | p.Arg100Ter | stop_gained | 6/17 | ENST00000307959.9 | |
ARR3 | XM_047442105.1 | c.322C>T | p.Arg108Ter | stop_gained | 5/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARR3 | ENST00000307959.9 | c.298C>T | p.Arg100Ter | stop_gained | 6/17 | 1 | NM_004312.3 | P1 | |
ARR3 | ENST00000374495.7 | c.298C>T | p.Arg100Ter | stop_gained | 6/16 | 1 | |||
ARR3 | ENST00000480877.6 | c.145C>T | p.Arg49Ter | stop_gained | 6/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome AF: 0.00000638 AC: 7AN: 1098025Hom.: 0 Cov.: 32 AF XY: 0.00000826 AC XY: 3AN XY: 363383
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
Myopia 26, X-linked, female-limited Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 22, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at