chr8-100162383-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003114.5(SPAG1):c.103G>A(p.Asp35Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000417 in 1,438,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D35E) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPAG1 | NM_003114.5 | c.103G>A | p.Asp35Asn | missense_variant | 2/19 | ENST00000388798.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPAG1 | ENST00000388798.7 | c.103G>A | p.Asp35Asn | missense_variant | 2/19 | 1 | NM_003114.5 | P1 | |
SPAG1 | ENST00000251809.4 | c.103G>A | p.Asp35Asn | missense_variant | 2/19 | 5 | P1 | ||
SPAG1 | ENST00000520508.5 | c.103G>A | p.Asp35Asn | missense_variant | 2/10 | 5 | |||
SPAG1 | ENST00000520643.5 | c.103G>A | p.Asp35Asn | missense_variant | 2/10 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000177 AC: 4AN: 226294Hom.: 0 AF XY: 0.0000327 AC XY: 4AN XY: 122318
GnomAD4 exome AF: 0.00000417 AC: 6AN: 1438030Hom.: 0 Cov.: 28 AF XY: 0.00000700 AC XY: 5AN XY: 714744
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.103G>A (p.D35N) alteration is located in exon 2 (coding exon 1) of the SPAG1 gene. This alteration results from a G to A substitution at nucleotide position 103, causing the aspartic acid (D) at amino acid position 35 to be replaced by an asparagine (N). 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