7-117229759-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001369598.1(ST7):c.1639-3C>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 0.000174 in 1,606,438 control chromosomes in the GnomAD database, including 2 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_001369598.1 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST7 | NM_001369598.1 | c.1639-3C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000323984.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST7 | ENST00000323984.8 | c.1639-3C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001369598.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000841 AC: 128AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000273 AC: 67AN: 245692Hom.: 0 AF XY: 0.000181 AC XY: 24AN XY: 132868
GnomAD4 exome AF: 0.000105 AC: 152AN: 1454122Hom.: 2 Cov.: 31 AF XY: 0.0000816 AC XY: 59AN XY: 722790
GnomAD4 genome ? AF: 0.000840 AC: 128AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000886 AC XY: 66AN XY: 74486
ClinVar
Submissions by phenotype
ST7-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 31, 2022 | This variant is classified as likely 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