rs397514695
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_014254.3(RXYLT1):c.1018C>A(p.Arg340=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R340R) has been classified as Likely benign.
Frequency
Consequence
NM_014254.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXYLT1 | NM_014254.3 | c.1018C>A | p.Arg340= | synonymous_variant | 6/6 | ENST00000261234.11 | |
RXYLT1 | NM_001278237.2 | c.238C>A | p.Arg80= | synonymous_variant | 6/6 | ||
RXYLT1 | XM_047428078.1 | c.709C>A | p.Arg237= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXYLT1 | ENST00000261234.11 | c.1018C>A | p.Arg340= | synonymous_variant | 6/6 | 1 | NM_014254.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250060Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135140
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461048Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726784
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74292
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at