rs1046934
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_052965.4(TSEN15):āc.177A>Cā(p.Gln59His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,603,524 control chromosomes in the GnomAD database, including 93,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_052965.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSEN15 | NM_052965.4 | c.177A>C | p.Gln59His | missense_variant | 2/5 | ENST00000645668.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSEN15 | ENST00000645668.2 | c.177A>C | p.Gln59His | missense_variant | 2/5 | NM_052965.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.289 AC: 43936AN: 151898Hom.: 6993 Cov.: 32
GnomAD3 exomes AF: 0.335 AC: 83944AN: 250454Hom.: 15007 AF XY: 0.338 AC XY: 45754AN XY: 135338
GnomAD4 exome AF: 0.340 AC: 494027AN: 1451508Hom.: 86655 Cov.: 30 AF XY: 0.340 AC XY: 245664AN XY: 722494
GnomAD4 genome AF: 0.289 AC: 43948AN: 152016Hom.: 6992 Cov.: 32 AF XY: 0.293 AC XY: 21784AN XY: 74302
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at