chrX-133303076-T-TA
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001448.3(GPC4):c.1469-8_1469-7insT 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 0.0000469 in 1,194,860 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001448.3 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 | UniProt |
---|---|---|---|---|---|---|---|
GPC4 | NM_001448.3 | c.1469-8_1469-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000370828.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC4 | ENST00000370828.4 | c.1469-8_1469-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001448.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000453 AC: 5AN: 110464Hom.: 0 Cov.: 23 AF XY: 0.0000303 AC XY: 1AN XY: 32992
GnomAD4 exome AF: 0.0000470 AC: 51AN: 1084396Hom.: 0 Cov.: 29 AF XY: 0.0000254 AC XY: 9AN XY: 354548
GnomAD4 genome ? AF: 0.0000453 AC: 5AN: 110464Hom.: 0 Cov.: 23 AF XY: 0.0000303 AC XY: 1AN XY: 32992
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at