chr17-3610700-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_013276.4(SHPK):c.1297G>A(p.Ala433Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000124 in 1,614,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A433A) has been classified as Likely benign.
Frequency
Consequence
NM_013276.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHPK | NM_013276.4 | c.1297G>A | p.Ala433Thr | missense_variant | Exon 7 of 7 | ENST00000225519.5 | NP_037408.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHPK | ENST00000225519.5 | c.1297G>A | p.Ala433Thr | missense_variant | Exon 7 of 7 | 1 | NM_013276.4 | ENSP00000225519.3 | ||
ENSG00000262304 | ENST00000572919.1 | n.1297G>A | non_coding_transcript_exon_variant | Exon 7 of 14 | 5 | ENSP00000461416.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251234Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135796
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461828Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727210
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1297G>A (p.A433T) alteration is located in exon 7 (coding exon 7) of the SHPK gene. This alteration results from a G to A substitution at nucleotide position 1297, causing the alanine (A) at amino acid position 433 to be replaced by a threonine (T). 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