rs79233884
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The ENST00000224140.6(SETX):āc.7101A>Gā(p.Gly2367=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000407 in 1,611,682 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
ENST00000224140.6 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SETX | NM_015046.7 | c.7101A>G | p.Gly2367= | splice_region_variant, synonymous_variant | 24/26 | ENST00000224140.6 | NP_055861.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SETX | ENST00000224140.6 | c.7101A>G | p.Gly2367= | splice_region_variant, synonymous_variant | 24/26 | 1 | NM_015046.7 | ENSP00000224140 | P1 | |
SETX | ENST00000436441.5 | c.1827A>G | p.Gly609= | splice_region_variant, synonymous_variant | 14/17 | 5 | ENSP00000409143 | |||
SETX | ENST00000477049.1 | n.128A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00143 AC: 218AN: 152136Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000549 AC: 138AN: 251386Hom.: 1 AF XY: 0.000427 AC XY: 58AN XY: 135860
GnomAD4 exome AF: 0.000299 AC: 437AN: 1459432Hom.: 4 Cov.: 30 AF XY: 0.000273 AC XY: 198AN XY: 726226
GnomAD4 genome AF: 0.00144 AC: 219AN: 152250Hom.: 1 Cov.: 32 AF XY: 0.00140 AC XY: 104AN XY: 74438
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jan 31, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 03, 2021 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | SETX: BP4, BP7 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2;C1865409:Amyotrophic lateral sclerosis type 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
Hereditary spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 01, 2019 | - - |
Amyotrophic lateral sclerosis type 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Feb 08, 2023 | - - |
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Feb 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at