rs3828161
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142644.2(SPHKAP):c.2600A>T(p.Gln867Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,904 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q867R) has been classified as Likely benign.
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.2600A>T | p.Gln867Leu | missense_variant | 7/12 | ENST00000392056.8 | |
LOC105373918 | XR_001739908.2 | n.147-8727T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPHKAP | ENST00000392056.8 | c.2600A>T | p.Gln867Leu | missense_variant | 7/12 | 1 | NM_001142644.2 | P2 | |
SPHKAP | ENST00000344657.5 | c.2600A>T | p.Gln867Leu | missense_variant | 7/11 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251372Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135850
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461870Hom.: 0 Cov.: 36 AF XY: 0.0000206 AC XY: 15AN XY: 727236
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74252
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at