chr17-3610786-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013276.4(SHPK):c.1211G>A(p.Arg404Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013276.4 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 |
---|---|---|---|---|---|---|---|
SHPK | NM_013276.4 | c.1211G>A | p.Arg404Gln | missense_variant | 7/7 | ENST00000225519.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHPK | ENST00000225519.5 | c.1211G>A | p.Arg404Gln | missense_variant | 7/7 | 1 | NM_013276.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251314Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135834
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461850Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727230
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 404 of the SHPK protein (p.Arg404Gln). This variant is present in population databases (rs371517274, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with SHPK-related conditions. ClinVar contains an entry for this variant (Variation ID: 2189889). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at