19-3586488-C-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_133261.3(GIPC3):c.226-7C>G 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 0.000554 in 1,612,884 control chromosomes in the GnomAD database, including 6 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 Benign (★★).
Frequency
Consequence
NM_133261.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GIPC3 | NM_133261.3 | c.226-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000644452.3 | NP_573568.1 | |||
GIPC3 | NM_001411144.1 | c.226-7C>G | 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>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_133261.3 | ENSP00000493901 | P1 | ||||
GIPC3 | ENST00000644946.1 | c.226-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENSP00000495068 |
Frequencies
GnomAD3 genomes AF: 0.000934 AC: 142AN: 152050Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00108 AC: 269AN: 249330Hom.: 2 AF XY: 0.000946 AC XY: 128AN XY: 135318
GnomAD4 exome AF: 0.000514 AC: 751AN: 1460716Hom.: 4 Cov.: 36 AF XY: 0.000480 AC XY: 349AN XY: 726664
GnomAD4 genome AF: 0.000933 AC: 142AN: 152168Hom.: 2 Cov.: 32 AF XY: 0.00141 AC XY: 105AN XY: 74408
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 06, 2016 | c.226-7C>G in intron 1 of GIPC3: This variant is not expected to have clinical s ignificance because it has been identified in 0.9% (57/6494) of Finnish chromoso mes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; d bSNP rs143968967). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at