2-227995626-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142644.2(SPHKAP):āc.4517C>Gā(p.Ala1506Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1506T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001142644.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPHKAP | NM_001142644.2 | c.4517C>G | p.Ala1506Gly | missense_variant | 8/12 | ENST00000392056.8 | |
LOC105373918 | XR_001739908.2 | n.147-31355G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPHKAP | ENST00000392056.8 | c.4517C>G | p.Ala1506Gly | missense_variant | 8/12 | 1 | NM_001142644.2 | P2 | |
SPHKAP | ENST00000344657.5 | c.4517C>G | p.Ala1506Gly | missense_variant | 8/11 | 1 | A2 | ||
SPHKAP | ENST00000490603.1 | n.10C>G | non_coding_transcript_exon_variant | 1/4 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250740Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135504
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461608Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727106
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at