1-172659333-GCCACCA-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000639.3(FASLG):c.141_146del(p.Pro52_Pro53del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,194 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P45P) has been classified as Likely benign.
Frequency
Consequence
NM_000639.3 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASLG | NM_000639.3 | c.141_146del | p.Pro52_Pro53del | inframe_deletion | 1/4 | ENST00000367721.3 | |
FASLG | NM_001302746.2 | c.141_146del | p.Pro52_Pro53del | inframe_deletion | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASLG | ENST00000367721.3 | c.141_146del | p.Pro52_Pro53del | inframe_deletion | 1/4 | 1 | NM_000639.3 | P1 | |
FASLG | ENST00000340030.4 | c.141_146del | p.Pro52_Pro53del | inframe_deletion | 1/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152046Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247688Hom.: 0 AF XY: 0.0000522 AC XY: 7AN XY: 134146
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1461030Hom.: 0 AF XY: 0.0000138 AC XY: 10AN XY: 726802
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74384
ClinVar
Submissions by phenotype
Autoimmune lymphoproliferative syndrome type 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 20, 2022 | This variant, c.141_146del, results in the deletion of 2 amino acid(s) of the FASLG protein (p.Pro52_Pro53del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs780931354, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with FASLG-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at