rs375262484
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_000391.4(TPP1):c.688-7T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000289 in 1,613,918 control chromosomes in the GnomAD database, including 1 homozygotes. 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_000391.4 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
TPP1 | NM_000391.4 | c.688-7T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000299427.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPP1 | ENST00000299427.12 | c.688-7T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000391.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00171 AC: 260AN: 152068Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000430 AC: 108AN: 251330Hom.: 1 AF XY: 0.000331 AC XY: 45AN XY: 135844
GnomAD4 exome AF: 0.000141 AC: 206AN: 1461732Hom.: 1 Cov.: 41 AF XY: 0.000110 AC XY: 80AN XY: 727172
GnomAD4 genome ? AF: 0.00172 AC: 261AN: 152186Hom.: 0 Cov.: 31 AF XY: 0.00177 AC XY: 132AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 14, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 23, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at