12-63780030-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014254.3(RXYLT1):c.70G>A(p.Ala24Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000412 in 1,456,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. A24P) has been classified as Uncertain significance.
Frequency
Consequence
NM_014254.3 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 |
---|---|---|---|---|---|---|---|
RXYLT1 | NM_014254.3 | c.70G>A | p.Ala24Thr | missense_variant | 1/6 | ENST00000261234.11 | |
RXYLT1 | XM_047428079.1 | c.70G>A | p.Ala24Thr | missense_variant | 1/5 | ||
RXYLT1 | NM_001278237.2 | c.-1044G>A | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXYLT1 | ENST00000261234.11 | c.70G>A | p.Ala24Thr | missense_variant | 1/6 | 1 | NM_014254.3 | P1 | |
ENST00000509615.2 | n.238+15451C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000815 AC: 2AN: 245386Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133234
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1456164Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 724712
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at