15-68945806-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145658.4(SPESP1):āc.272C>Gā(p.Thr91Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,772 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. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_145658.4 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 |
---|---|---|---|---|---|---|---|
SPESP1 | NM_145658.4 | c.272C>G | p.Thr91Ser | missense_variant | 2/2 | ENST00000310673.4 | |
NOX5 | NM_001184780.2 | c.29+15089C>G | intron_variant | ||||
NOX5 | NR_033671.3 | n.193+15089C>G | intron_variant, non_coding_transcript_variant | ||||
NOX5 | NR_033672.2 | n.193+15089C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPESP1 | ENST00000310673.4 | c.272C>G | p.Thr91Ser | missense_variant | 2/2 | 1 | NM_145658.4 | P1 | |
SPESP1 | ENST00000560188.1 | n.305C>G | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
SPESP1 | ENST00000561467.1 | n.268C>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000178 AC: 27AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250716Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135540
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461736Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727172
GnomAD4 genome AF: 0.000178 AC: 27AN: 152036Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.272C>G (p.T91S) alteration is located in exon 2 (coding exon 2) of the SPESP1 gene. This alteration results from a C to G substitution at nucleotide position 272, causing the threonine (T) at amino acid position 91 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