22-39025649-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152426.4(APOBEC3D):c.583C>T(p.Arg195Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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_152426.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOBEC3D | NM_152426.4 | c.583C>T | p.Arg195Cys | missense_variant | Exon 4 of 7 | ENST00000216099.13 | NP_689639.2 | |
APOBEC3D | XM_017028596.3 | c.790C>T | p.Arg264Cys | missense_variant | Exon 3 of 6 | XP_016884085.1 | ||
APOBEC3D | XM_047441142.1 | c.583C>T | p.Arg195Cys | missense_variant | Exon 4 of 5 | XP_047297098.1 | ||
APOBEC3D | NM_001363781.1 | c.210+2635C>T | 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.583C>T | p.Arg195Cys | missense_variant | Exon 4 of 7 | 2 | NM_152426.4 | ENSP00000216099.7 | ||
ENSG00000284554 | ENST00000381568.9 | c.583C>T | p.Arg195Cys | missense_variant | Exon 4 of 7 | 1 | ENSP00000370980.4 | |||
APOBEC3D | ENST00000427494.6 | c.210+2635C>T | intron_variant | Intron 2 of 3 | 1 | ENSP00000388017.2 | ||||
APOBEC3D | ENST00000622217.3 | c.18-3714C>T | intron_variant | Intron 1 of 3 | 5 | ENSP00000480718.3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152124Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251462Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135908
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461870Hom.: 0 Cov.: 34 AF XY: 0.0000206 AC XY: 15AN XY: 727244
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.583C>T (p.R195C) alteration is located in exon 4 (coding exon 4) of the APOBEC3D gene. This alteration results from a C to T substitution at nucleotide position 583, causing the arginine (R) at amino acid position 195 to be replaced by a cysteine (C). 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