7-44002800-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001378423.2(SPDYE1):c.590C>T(p.Ala197Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000256 in 1,522,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001378423.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPDYE1 | NM_001378423.2 | c.590C>T | p.Ala197Val | missense_variant | Exon 4 of 9 | ENST00000693451.1 | NP_001365352.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPDYE1 | ENST00000693451.1 | c.590C>T | p.Ala197Val | missense_variant | Exon 4 of 9 | NM_001378423.2 | ENSP00000509569.1 |
Frequencies
GnomAD3 genomes AF: 0.00000926 AC: 1AN: 108002Hom.: 0 Cov.: 15
GnomAD3 exomes AF: 0.0000251 AC: 5AN: 198846Hom.: 0 AF XY: 0.0000276 AC XY: 3AN XY: 108560
GnomAD4 exome AF: 0.0000269 AC: 38AN: 1414804Hom.: 0 Cov.: 28 AF XY: 0.0000270 AC XY: 19AN XY: 702658
GnomAD4 genome AF: 0.00000926 AC: 1AN: 108002Hom.: 0 Cov.: 15 AF XY: 0.0000199 AC XY: 1AN XY: 50218
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.470C>T (p.A157V) alteration is located in exon 2 (coding exon 2) of the SPDYE1 gene. This alteration results from a C to T substitution at nucleotide position 470, causing the alanine (A) at amino acid position 157 to be replaced by a valine (V). 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