rs150016894
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_144991.3(TSPEAR):c.151G>A(p.Val51Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,593,350 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_144991.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPEAR | NM_144991.3 | c.151G>A | p.Val51Ile | missense_variant | 2/12 | ENST00000323084.9 | |
TSPEAR | NM_001272037.2 | c.-54G>A | 5_prime_UTR_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPEAR | ENST00000323084.9 | c.151G>A | p.Val51Ile | missense_variant | 2/12 | 1 | NM_144991.3 | P1 | |
TSPEAR | ENST00000397916.1 | n.106G>A | non_coding_transcript_exon_variant | 2/11 | 1 | ||||
TSPEAR | ENST00000642437.1 | c.*96G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/13 |
Frequencies
GnomAD3 genomes ? AF: 0.00129 AC: 196AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 255AN: 242878Hom.: 0 AF XY: 0.00113 AC XY: 148AN XY: 131308
GnomAD4 exome AF: 0.00171 AC: 2470AN: 1441078Hom.: 3 Cov.: 30 AF XY: 0.00170 AC XY: 1217AN XY: 714966
GnomAD4 genome ? AF: 0.00129 AC: 196AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.00113 AC XY: 84AN XY: 74468
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 04, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 20, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 04, 2015 | p.Val51Ile in exon 2 of TSPEAR: This variant is not expected to have clinical si gnificance due to a lack of conservation across species, including mammals. Of n ote, 6 mammals have an isoleucine (Ile) at this position. In addition, computati onal prediction tools do not suggest a high likelihood of impact to the protein. Furthermore, this variant has been identified in 0.15% (97/65584) of European c hromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute .org; dbSNP rs150016894). - |
TSPEAR-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 16, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at