9-136433146-C-CGCGCCCACCCCTCCAGCT
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_019892.6(INPP5E):c.1159+8_1159+9insAGCTGGAGGGGTGGGCGC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,608,090 control chromosomes in the GnomAD database, including 37 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_019892.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INPP5E | ENST00000371712.4 | c.1159+8_1159+9insAGCTGGAGGGGTGGGCGC | splice_region_variant, intron_variant | Intron 4 of 9 | 1 | NM_019892.6 | ENSP00000360777.3 | |||
INPP5E | ENST00000676019.1 | c.1057+8_1057+9insAGCTGGAGGGGTGGGCGC | splice_region_variant, intron_variant | Intron 4 of 9 | ENSP00000501984.1 |
Frequencies
GnomAD3 genomes AF: 0.00930 AC: 1410AN: 151606Hom.: 20 Cov.: 30
GnomAD3 exomes AF: 0.00220 AC: 526AN: 239056Hom.: 6 AF XY: 0.00173 AC XY: 226AN XY: 130476
GnomAD4 exome AF: 0.000899 AC: 1309AN: 1456366Hom.: 17 Cov.: 42 AF XY: 0.000776 AC XY: 562AN XY: 724694
GnomAD4 genome AF: 0.00931 AC: 1413AN: 151724Hom.: 20 Cov.: 30 AF XY: 0.00932 AC XY: 691AN XY: 74154
ClinVar
Submissions by phenotype
not specified Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:1
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Familial aplasia of the vermis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at