22-39025112-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152426.4(APOBEC3D):c.253T>C(p.Ser85Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,458,404 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOBEC3D | NM_152426.4 | c.253T>C | p.Ser85Pro | missense_variant | Exon 3 of 7 | ENST00000216099.13 | NP_689639.2 | |
APOBEC3D | XM_017028596.3 | c.253T>C | p.Ser85Pro | missense_variant | Exon 3 of 6 | XP_016884085.1 | ||
APOBEC3D | XM_047441142.1 | c.253T>C | p.Ser85Pro | missense_variant | Exon 3 of 5 | XP_047297098.1 | ||
APOBEC3D | NM_001363781.1 | c.210+2098T>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.253T>C | p.Ser85Pro | missense_variant | Exon 3 of 7 | 2 | NM_152426.4 | ENSP00000216099.7 | ||
ENSG00000284554 | ENST00000381568.9 | c.253T>C | p.Ser85Pro | missense_variant | Exon 3 of 7 | 1 | ENSP00000370980.4 | |||
APOBEC3D | ENST00000427494.6 | c.210+2098T>C | intron_variant | Intron 2 of 3 | 1 | ENSP00000388017.2 | ||||
APOBEC3D | ENST00000622217.3 | c.17+3576T>C | intron_variant | Intron 1 of 3 | 5 | ENSP00000480718.3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248734Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134474
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1458404Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 725136
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.253T>C (p.S85P) 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 253, causing the serine (S) at amino acid position 85 to be replaced by a proline (P). 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