19-33210493-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_019849.3(SLC7A10):c.1237C>T(p.Arg413Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,604,426 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R413Q) has been classified as Likely benign.
Frequency
Consequence
NM_019849.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC7A10 | NM_019849.3 | c.1237C>T | p.Arg413Trp | missense_variant | 9/11 | ENST00000253188.8 | NP_062823.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC7A10 | ENST00000253188.8 | c.1237C>T | p.Arg413Trp | missense_variant | 9/11 | 1 | NM_019849.3 | ENSP00000253188.2 | ||
SLC7A10 | ENST00000590036.5 | n.1140C>T | non_coding_transcript_exon_variant | 8/10 | 5 | ENSP00000465421.1 | ||||
SLC7A10 | ENST00000590490.1 | n.1012C>T | non_coding_transcript_exon_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000295 AC: 7AN: 236994Hom.: 0 AF XY: 0.0000465 AC XY: 6AN XY: 129130
GnomAD4 exome AF: 0.0000152 AC: 22AN: 1452104Hom.: 0 Cov.: 33 AF XY: 0.0000180 AC XY: 13AN XY: 722376
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.1237C>T (p.R413W) alteration is located in exon 9 (coding exon 9) of the SLC7A10 gene. This alteration results from a C to T substitution at nucleotide position 1237, causing the arginine (R) at amino acid position 413 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at