NM_017934.7:c.5284T>C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_017934.7(PHIP):c.5284T>C(p.Ser1762Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000279 in 1,613,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S1762S) has been classified as Likely benign.
Frequency
Consequence
NM_017934.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHIP | NM_017934.7 | c.5284T>C | p.Ser1762Pro | missense_variant | Exon 40 of 40 | ENST00000275034.5 | NP_060404.4 | |
PHIP | XM_005248729.6 | c.5281T>C | p.Ser1761Pro | missense_variant | Exon 40 of 40 | XP_005248786.1 | ||
PHIP | XM_011535918.4 | c.4768T>C | p.Ser1590Pro | missense_variant | Exon 37 of 37 | XP_011534220.1 | ||
IRAK1BP1 | XM_047418194.1 | c.*37+5306A>G | intron_variant | Intron 3 of 3 | XP_047274150.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151996Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251190Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135756
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461778Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727182
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151996Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74258
ClinVar
Submissions by phenotype
not provided Benign:1
PHIP: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at