chr2-227995618-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142644.2(SPHKAP):c.4525C>A(p.Pro1509Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001142644.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPHKAP | NM_001142644.2 | c.4525C>A | p.Pro1509Thr | missense_variant | 8/12 | ENST00000392056.8 | NP_001136116.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPHKAP | ENST00000392056.8 | c.4525C>A | p.Pro1509Thr | missense_variant | 8/12 | 1 | NM_001142644.2 | ENSP00000375909.3 | ||
SPHKAP | ENST00000344657.5 | c.4525C>A | p.Pro1509Thr | missense_variant | 8/11 | 1 | ENSP00000339886.5 | |||
SPHKAP | ENST00000490603.1 | n.18C>A | non_coding_transcript_exon_variant | 1/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250998Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135634
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461754Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727180
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2023 | The c.4525C>A (p.P1509T) alteration is located in exon 8 (coding exon 8) of the SPHKAP gene. This alteration results from a C to A substitution at nucleotide position 4525, causing the proline (P) at amino acid position 1509 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