rs117034581
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3BP6
The NM_144991.3(TSPEAR):c.1566+5G>A variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.0019 in 1,612,918 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_144991.3 splice_donor_5th_base, intron
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 |
---|---|---|---|---|---|---|---|
TSPEAR | NM_144991.3 | c.1566+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.1362+5G>A | splice_donor_5th_base_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPEAR | ENST00000323084.9 | c.1566+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000397916.1 | n.1521+5G>A | splice_donor_5th_base_variant, intron_variant, non_coding_transcript_variant | 1 | |||||
TSPEAR-AS2 | ENST00000465978.1 | n.217-3946C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
TSPEAR | ENST00000642437.1 | c.*1511+5G>A | splice_donor_5th_base_variant, intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00137 AC: 209AN: 152106Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00109 AC: 274AN: 250250Hom.: 0 AF XY: 0.00102 AC XY: 138AN XY: 135366
GnomAD4 exome AF: 0.00195 AC: 2849AN: 1460694Hom.: 4 Cov.: 32 AF XY: 0.00189 AC XY: 1374AN XY: 726546
GnomAD4 genome ? AF: 0.00137 AC: 209AN: 152224Hom.: 1 Cov.: 33 AF XY: 0.00121 AC XY: 90AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | TSPEAR: BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 27, 2021 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 02, 2016 | Variant classified as Uncertain Significance - Favor Benign. The c.1566+5G>A var iant in TSPEAR has not been previously reported in individuals with hearing loss , but has been identified in 0.2% (112/65824) of European chromosomes by the Exo me Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs1170345 81). This variant is located in the 5' splice region. Computational tools do not suggest an impact to splicing. However, this information is not predictive enou gh to rule out pathogenicity. In summary, while the clinical significance of the c.1566+5G>A variant is uncertain, its frequency suggests that it is more likely to be benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at