6-78990442-A-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_017934.7(PHIP):c.2319+426T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 31)
Failed GnomAD Quality Control
Consequence
PHIP
NM_017934.7 intron
NM_017934.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.319
Genes affected
PHIP (HGNC:15673): (pleckstrin homology domain interacting protein) This gene encodes a protein that binds to the insulin receptor substrate 1 protein and regulates glucose transporter translocation in skeletal muscle cells. The encoded protein may also regulate growth and survival of pancreatic beta cells. Elevated copy number of this gene may be associated with melanoma severity and the encoded protein may promote melanoma metastasis in human patients. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHIP | NM_017934.7 | c.2319+426T>A | intron_variant | Intron 20 of 39 | ENST00000275034.5 | NP_060404.4 | ||
PHIP | XM_005248729.6 | c.2316+426T>A | intron_variant | Intron 20 of 39 | XP_005248786.1 | |||
PHIP | XM_011535918.4 | c.1803+426T>A | intron_variant | Intron 17 of 36 | XP_011534220.1 | |||
PHIP | XM_011535919.2 | c.2319+426T>A | intron_variant | Intron 20 of 25 | XP_011534221.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152078Hom.: 0 Cov.: 31 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 152078Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74278
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at