chr17-58310934-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004758.4(TSPOAP1):c.3361C>T(p.Pro1121Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,564,370 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004758.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPOAP1 | NM_004758.4 | c.3361C>T | p.Pro1121Ser | missense_variant | 19/32 | ENST00000343736.9 | |
TSPOAP1 | NM_001261835.2 | c.3361C>T | p.Pro1121Ser | missense_variant | 19/32 | ||
TSPOAP1 | NM_024418.3 | c.3181C>T | p.Pro1061Ser | missense_variant | 18/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPOAP1 | ENST00000343736.9 | c.3361C>T | p.Pro1121Ser | missense_variant | 19/32 | 1 | NM_004758.4 | P2 | |
TSPOAP1 | ENST00000268893.10 | c.3181C>T | p.Pro1061Ser | missense_variant | 18/31 | 1 | A2 | ||
TSPOAP1 | ENST00000580669.6 | c.757C>T | p.Pro253Ser | missense_variant | 3/16 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00169 AC: 257AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00127 AC: 258AN: 203790Hom.: 0 AF XY: 0.00129 AC XY: 143AN XY: 110944
GnomAD4 exome AF: 0.00171 AC: 2408AN: 1412054Hom.: 5 Cov.: 34 AF XY: 0.00162 AC XY: 1136AN XY: 699406
GnomAD4 genome ? AF: 0.00169 AC: 257AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.00160 AC XY: 119AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at