chr4-25804749-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015187.5(SEL1L3):c.1568C>T(p.Pro523Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,608,110 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 (★).
Frequency
Consequence
NM_015187.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEL1L3 | NM_015187.5 | c.1568C>T | p.Pro523Leu | missense_variant | 10/24 | ENST00000399878.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEL1L3 | ENST00000399878.8 | c.1568C>T | p.Pro523Leu | missense_variant | 10/24 | 1 | NM_015187.5 | P1 | |
SEL1L3 | ENST00000264868.9 | c.1463C>T | p.Pro488Leu | missense_variant | 10/24 | 1 | |||
SEL1L3 | ENST00000502949.5 | c.1109C>T | p.Pro370Leu | missense_variant | 10/24 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249022Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135106
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1455836Hom.: 0 Cov.: 30 AF XY: 0.00000552 AC XY: 4AN XY: 724648
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.1568C>T (p.P523L) alteration is located in exon 10 (coding exon 10) of the SEL1L3 gene. This alteration results from a C to T substitution at nucleotide position 1568, causing the proline (P) at amino acid position 523 to be replaced by a leucine (L). 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