rs150091333
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001330723.2(SNX27):c.984T>C(p.Phe328=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000834 in 1,609,738 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001330723.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX27 | NM_001330723.2 | c.984T>C | p.Phe328= | splice_region_variant, synonymous_variant | 6/12 | ENST00000458013.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX27 | ENST00000458013.7 | c.984T>C | p.Phe328= | splice_region_variant, synonymous_variant | 6/12 | 5 | NM_001330723.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00411 AC: 626AN: 152252Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00119 AC: 298AN: 249520Hom.: 3 AF XY: 0.000867 AC XY: 117AN XY: 134902
GnomAD4 exome AF: 0.000490 AC: 714AN: 1457368Hom.: 6 Cov.: 29 AF XY: 0.000466 AC XY: 338AN XY: 725004
GnomAD4 genome ? AF: 0.00412 AC: 628AN: 152370Hom.: 2 Cov.: 32 AF XY: 0.00380 AC XY: 283AN XY: 74510
ClinVar
Submissions by phenotype
Severe myoclonic epilepsy in infancy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
SNX27-related condition Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at