rs141095352
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000261234.11(RXYLT1):āc.252C>Gā(p.Ser84Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,456,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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. S84G) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000261234.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RXYLT1 | NM_014254.3 | c.252C>G | p.Ser84Arg | missense_variant | 2/6 | ENST00000261234.11 | NP_055069.1 | |
RXYLT1 | XM_047428079.1 | c.252C>G | p.Ser84Arg | missense_variant | 2/5 | XP_047284035.1 | ||
RXYLT1 | NM_001278237.2 | c.-529C>G | 5_prime_UTR_variant | 2/6 | NP_001265166.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RXYLT1 | ENST00000261234.11 | c.252C>G | p.Ser84Arg | missense_variant | 2/6 | 1 | NM_014254.3 | ENSP00000261234 | P1 | |
ENST00000509615.2 | n.238+14380G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1456682Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 724614
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at