chr19-3586488-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_133261.3(GIPC3):c.226-7C>T 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 0.0000149 in 1,612,770 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_133261.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GIPC3 | NM_133261.3 | c.226-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000644452.3 | NP_573568.1 | |||
GIPC3 | NM_001411144.1 | c.226-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001398073.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GIPC3 | ENST00000644452.3 | c.226-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_133261.3 | ENSP00000493901 | P1 | ||||
GIPC3 | ENST00000644946.1 | c.226-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENSP00000495068 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249330Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135318
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460720Hom.: 0 Cov.: 36 AF XY: 0.0000124 AC XY: 9AN XY: 726666
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74280
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at