1-183648649-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_203454.3(APOBEC4):c.133C>T(p.Leu45Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,056 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_203454.3 missense
Scores
Clinical Significance
Conservation
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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 |
---|---|---|---|---|---|---|---|---|---|---|
APOBEC4 | ENST00000308641.6 | c.133C>T | p.Leu45Phe | missense_variant | Exon 2 of 2 | 1 | NM_203454.3 | ENSP00000310622.4 | ||
RGL1 | ENST00000304685.8 | c.-33+12148G>A | intron_variant | Intron 1 of 18 | 1 | ENSP00000303192.3 | ||||
APOBEC4 | ENST00000481562.1 | n.246-852C>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251400Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135874
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461876Hom.: 0 Cov.: 33 AF XY: 0.0000523 AC XY: 38AN XY: 727238
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.133C>T (p.L45F) alteration is located in exon 2 (coding exon 1) of the APOBEC4 gene. This alteration results from a C to T substitution at nucleotide position 133, causing the leucine (L) at amino acid position 45 to be replaced by a phenylalanine (F). 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