rs28531779
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The XM_047433397.1(LOC124903441):c.41-13C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000183 in 328,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
XM_047433397.1 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124903441 | XM_047433397.1 | c.41-13C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA7 | ENST00000635884.1 | c.-132+427G>A | intron_variant | 5 | |||||
CHRNA7 | ENST00000635978.1 | c.-42-70902G>A | intron_variant | 5 | |||||
CHRNA7 | ENST00000636603.1 | c.-131-497G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000706 AC: 1AN: 141684Hom.: 0 Cov.: 19
GnomAD4 exome AF: 0.0000268 AC: 5AN: 186504Hom.: 0 AF XY: 0.0000317 AC XY: 3AN XY: 94698
GnomAD4 genome AF: 0.00000706 AC: 1AN: 141684Hom.: 0 Cov.: 19 AF XY: 0.0000145 AC XY: 1AN XY: 68930
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at