15-45402535-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_024063.3(AFG2B):c.106C>T(p.Leu36Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000188 in 1,597,444 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 Likely benign (★).
Frequency
Consequence
NM_024063.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATA5L1 | ENST00000305560.11 | c.106C>T | p.Leu36Phe | missense_variant | Exon 1 of 8 | 1 | NM_024063.3 | ENSP00000305494.6 | ||
SPATA5L1 | ENST00000531970.5 | n.106C>T | non_coding_transcript_exon_variant | Exon 1 of 8 | 2 | ENSP00000436823.1 | ||||
SPATA5L1 | ENST00000559860.2 | n.166C>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 2 | |||||
GATM | ENST00000458245.5 | n.-208G>A | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1445204Hom.: 0 Cov.: 33 AF XY: 0.00000139 AC XY: 1AN XY: 717990
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at