rs144105303
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000639.3(FASLG):c.828C>T(p.Phe276=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 1,614,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
FASLG
NM_000639.3 synonymous
NM_000639.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.155
Genes affected
FASLG (HGNC:11936): (Fas ligand) This gene is a member of the tumor necrosis factor superfamily. The primary function of the encoded transmembrane protein is the induction of apoptosis triggered by binding to FAS. The FAS/FASLG signaling pathway is essential for immune system regulation, including activation-induced cell death (AICD) of T cells and cytotoxic T lymphocyte induced cell death. It has also been implicated in the progression of several cancers. Defects in this gene may be related to some cases of systemic lupus erythematosus (SLE). Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 1-172665998-C-T is Benign according to our data. Variant chr1-172665998-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 532233.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.155 with no splicing effect.
BS2
High AC in GnomAd4 at 41 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FASLG | NM_000639.3 | c.828C>T | p.Phe276= | synonymous_variant | 4/4 | ENST00000367721.3 | NP_000630.1 | |
FASLG | NM_001302746.2 | c.*398C>T | 3_prime_UTR_variant | 3/3 | NP_001289675.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FASLG | ENST00000367721.3 | c.828C>T | p.Phe276= | synonymous_variant | 4/4 | 1 | NM_000639.3 | ENSP00000356694 | P1 | |
FASLG | ENST00000340030.4 | c.*398C>T | 3_prime_UTR_variant | 3/3 | 1 | ENSP00000344739 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152146Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000227 AC: 57AN: 251148Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135728
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GnomAD4 exome AF: 0.000141 AC: 206AN: 1461838Hom.: 0 Cov.: 33 AF XY: 0.000133 AC XY: 97AN XY: 727232
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GnomAD4 genome AF: 0.000269 AC: 41AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74466
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autoimmune lymphoproliferative syndrome type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 06, 2024 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at