20-13534052-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_017714.3(TASP1):c.765G>A(p.Leu255Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 1,613,410 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_017714.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TASP1 | ENST00000337743.9 | c.765G>A | p.Leu255Leu | synonymous_variant | Exon 9 of 14 | 1 | NM_017714.3 | ENSP00000338624.4 | ||
TASP1 | ENST00000455532.5 | c.696G>A | p.Leu232Leu | synonymous_variant | Exon 8 of 10 | 5 | ENSP00000400580.1 | |||
TASP1 | ENST00000465381.5 | n.662G>A | non_coding_transcript_exon_variant | Exon 7 of 10 | 5 | |||||
TASP1 | ENST00000480436.5 | n.849G>A | non_coding_transcript_exon_variant | Exon 9 of 14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00324 AC: 492AN: 152072Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00607 AC: 1522AN: 250782Hom.: 16 AF XY: 0.00535 AC XY: 725AN XY: 135502
GnomAD4 exome AF: 0.00377 AC: 5502AN: 1461220Hom.: 35 Cov.: 30 AF XY: 0.00376 AC XY: 2730AN XY: 726918
GnomAD4 genome AF: 0.00324 AC: 493AN: 152190Hom.: 2 Cov.: 32 AF XY: 0.00348 AC XY: 259AN XY: 74396
ClinVar
Submissions by phenotype
TASP1-related disorder Benign:1
This variant is classified as 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