22-39025218-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_152426.4(APOBEC3D):c.359T>C(p.Leu120Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOBEC3D | NM_152426.4 | c.359T>C | p.Leu120Ser | missense_variant | Exon 3 of 7 | ENST00000216099.13 | NP_689639.2 | |
APOBEC3D | XM_017028596.3 | c.359T>C | p.Leu120Ser | missense_variant | Exon 3 of 6 | XP_016884085.1 | ||
APOBEC3D | XM_047441142.1 | c.359T>C | p.Leu120Ser | missense_variant | Exon 3 of 5 | XP_047297098.1 | ||
APOBEC3D | NM_001363781.1 | c.210+2204T>C | intron_variant | Intron 2 of 3 | NP_001350710.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOBEC3D | ENST00000216099.13 | c.359T>C | p.Leu120Ser | missense_variant | Exon 3 of 7 | 2 | NM_152426.4 | ENSP00000216099.7 | ||
ENSG00000284554 | ENST00000381568.9 | c.359T>C | p.Leu120Ser | missense_variant | Exon 3 of 7 | 1 | ENSP00000370980.4 | |||
APOBEC3D | ENST00000427494.6 | c.210+2204T>C | intron_variant | Intron 2 of 3 | 1 | ENSP00000388017.2 | ||||
APOBEC3D | ENST00000622217.3 | c.17+3682T>C | intron_variant | Intron 1 of 3 | 5 | ENSP00000480718.3 |
Frequencies
GnomAD3 genomes AF: 0.0000790 AC: 12AN: 151990Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251414Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135898
GnomAD4 exome AF: 0.000166 AC: 243AN: 1461856Hom.: 0 Cov.: 34 AF XY: 0.000142 AC XY: 103AN XY: 727238
GnomAD4 genome AF: 0.0000790 AC: 12AN: 151990Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.359T>C (p.L120S) alteration is located in exon 3 (coding exon 3) of the APOBEC3D gene. This alteration results from a T to C substitution at nucleotide position 359, causing the leucine (L) at amino acid position 120 to be replaced by a serine (S). 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