rs777488014
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003114.5(SPAG1):c.977C>T(p.Ser326Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000188 in 1,591,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003114.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPAG1 | ENST00000388798.7 | c.977C>T | p.Ser326Phe | missense_variant | Exon 10 of 19 | 1 | NM_003114.5 | ENSP00000373450.3 | ||
SPAG1 | ENST00000251809.4 | c.977C>T | p.Ser326Phe | missense_variant | Exon 10 of 19 | 5 | ENSP00000251809.3 | |||
SPAG1 | ENST00000520508.5 | c.977C>T | p.Ser326Phe | missense_variant | Exon 10 of 10 | 5 | ENSP00000428070.1 | |||
SPAG1 | ENST00000520643.5 | c.977C>T | p.Ser326Phe | missense_variant | Exon 10 of 10 | 2 | ENSP00000427716.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152082Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000170 AC: 4AN: 235680Hom.: 0 AF XY: 0.0000157 AC XY: 2AN XY: 127374
GnomAD4 exome AF: 0.0000194 AC: 28AN: 1439876Hom.: 0 Cov.: 29 AF XY: 0.0000168 AC XY: 12AN XY: 715328
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152082Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74296
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 28 Uncertain:1
This variant has not been reported in the literature in individuals affected with SPAG1-related conditions. This sequence change replaces serine with phenylalanine at codon 326 of the SPAG1 protein (p.Ser326Phe). The serine residue is weakly conserved and there is a large physicochemical difference between serine and phenylalanine. This variant is present in population databases (rs777488014, ExAC 0.002%). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at