chr4-25804723-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015187.5(SEL1L3):c.1594G>C(p.Glu532Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000304 in 1,613,628 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_015187.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEL1L3 | NM_015187.5 | c.1594G>C | p.Glu532Gln | missense_variant | 10/24 | ENST00000399878.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEL1L3 | ENST00000399878.8 | c.1594G>C | p.Glu532Gln | missense_variant | 10/24 | 1 | NM_015187.5 | P1 | |
SEL1L3 | ENST00000264868.9 | c.1489G>C | p.Glu497Gln | missense_variant | 10/24 | 1 | |||
SEL1L3 | ENST00000502949.5 | c.1135G>C | p.Glu379Gln | missense_variant | 10/24 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000136 AC: 34AN: 249174Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 135188
GnomAD4 exome AF: 0.000318 AC: 465AN: 1461306Hom.: 0 Cov.: 31 AF XY: 0.000283 AC XY: 206AN XY: 726988
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1594G>C (p.E532Q) alteration is located in exon 10 (coding exon 10) of the SEL1L3 gene. This alteration results from a G to C substitution at nucleotide position 1594, causing the glutamic acid (E) at amino acid position 532 to be replaced by a glutamine (Q). 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