10-119823880-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014937.4(INPP5F):c.2227A>G(p.Ile743Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000163 in 1,613,658 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014937.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INPP5F | NM_014937.4 | c.2227A>G | p.Ile743Val | missense_variant | 19/20 | ENST00000650623.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INPP5F | ENST00000650623.2 | c.2227A>G | p.Ile743Val | missense_variant | 19/20 | NM_014937.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251116Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135750
GnomAD4 exome AF: 0.000170 AC: 248AN: 1461508Hom.: 0 Cov.: 30 AF XY: 0.000160 AC XY: 116AN XY: 727078
GnomAD4 genome ? AF: 0.0000986 AC: 15AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 05, 2023 | The c.2227A>G (p.I743V) alteration is located in exon 19 (coding exon 19) of the INPP5F gene. This alteration results from a A to G substitution at nucleotide position 2227, causing the isoleucine (I) at amino acid position 743 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at