rs370342380
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_139058.3(ARX):c.148T>C(p.Leu50=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,209,215 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. 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. L50L) has been classified as Likely benign.
Frequency
Consequence
NM_139058.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARX | NM_139058.3 | c.148T>C | p.Leu50= | synonymous_variant | 1/5 | ENST00000379044.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARX | ENST00000379044.5 | c.148T>C | p.Leu50= | synonymous_variant | 1/5 | 1 | NM_139058.3 | P1 | |
ARX | ENST00000636609.1 | n.91T>C | non_coding_transcript_exon_variant | 2/2 | 5 | ||||
ARX | ENST00000637394.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000142 AC: 16AN: 112628Hom.: 0 Cov.: 24 AF XY: 0.000144 AC XY: 5AN XY: 34788
GnomAD3 exomes AF: 0.0000508 AC: 9AN: 177247Hom.: 0 AF XY: 0.0000791 AC XY: 5AN XY: 63203
GnomAD4 exome AF: 0.0000164 AC: 18AN: 1096587Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 5AN XY: 362135
GnomAD4 genome ? AF: 0.000142 AC: 16AN: 112628Hom.: 0 Cov.: 24 AF XY: 0.000144 AC XY: 5AN XY: 34788
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 24, 2018 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2020 | - - |
Intellectual disability, X-linked, with or without seizures, arx-related;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
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