15-68946436-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_145658.4(SPESP1):c.902A>G(p.Asn301Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145658.4 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 |
---|---|---|---|---|---|---|---|
SPESP1 | NM_145658.4 | c.902A>G | p.Asn301Ser | missense_variant | 2/2 | ENST00000310673.4 | |
NOX5 | NM_001184780.2 | c.29+15719A>G | intron_variant | ||||
NOX5 | NR_033671.3 | n.193+15719A>G | intron_variant, non_coding_transcript_variant | ||||
NOX5 | NR_033672.2 | n.193+15719A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPESP1 | ENST00000310673.4 | c.902A>G | p.Asn301Ser | missense_variant | 2/2 | 1 | NM_145658.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151734Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250434Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135694
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461300Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 726960
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151734Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74150
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.902A>G (p.N301S) alteration is located in exon 2 (coding exon 2) of the SPESP1 gene. This alteration results from a A to G substitution at nucleotide position 902, causing the asparagine (N) at amino acid position 301 to be replaced by a serine (S). 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