15-68945798-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145658.4(SPESP1):c.264T>A(p.Asp88Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,678 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_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.264T>A | p.Asp88Glu | missense_variant | 2/2 | ENST00000310673.4 | |
NOX5 | NM_001184780.2 | c.29+15081T>A | intron_variant | ||||
NOX5 | NR_033671.3 | n.193+15081T>A | intron_variant, non_coding_transcript_variant | ||||
NOX5 | NR_033672.2 | n.193+15081T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPESP1 | ENST00000310673.4 | c.264T>A | p.Asp88Glu | missense_variant | 2/2 | 1 | NM_145658.4 | P1 | |
SPESP1 | ENST00000560188.1 | n.297T>A | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
SPESP1 | ENST00000561467.1 | n.260T>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250754Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135540
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461678Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727144
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.264T>A (p.D88E) alteration is located in exon 2 (coding exon 2) of the SPESP1 gene. This alteration results from a T to A substitution at nucleotide position 264, causing the aspartic acid (D) at amino acid position 88 to be replaced by a glutamic acid (E). 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