chr2-217804603-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001387777.1(TNS1):c.5376G>A(p.Lys1792=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,614,012 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_001387777.1 splice_region, synonymous
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 |
---|---|---|---|---|---|---|---|
TNS1 | NM_001387777.1 | c.5376G>A | p.Lys1792= | splice_region_variant, synonymous_variant | 33/33 | ENST00000682258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNS1 | ENST00000682258.1 | c.5376G>A | p.Lys1792= | splice_region_variant, synonymous_variant | 33/33 | NM_001387777.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152200Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000923 AC: 23AN: 249130Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134816
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461694Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727166
GnomAD4 genome AF: 0.000269 AC: 41AN: 152318Hom.: 0 Cov.: 31 AF XY: 0.000255 AC XY: 19AN XY: 74474
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at