22-39029380-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152426.4(APOBEC3D):āc.623T>Cā(p.Met208Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOBEC3D | NM_152426.4 | c.623T>C | p.Met208Thr | missense_variant | Exon 5 of 7 | ENST00000216099.13 | NP_689639.2 | |
APOBEC3D | XM_017028596.3 | c.830T>C | p.Met277Thr | missense_variant | Exon 4 of 6 | XP_016884085.1 | ||
APOBEC3D | NM_001363781.1 | c.211-2314T>C | intron_variant | Intron 2 of 3 | NP_001350710.1 | |||
APOBEC3D | XM_047441142.1 | c.606-2314T>C | intron_variant | Intron 4 of 4 | XP_047297098.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOBEC3D | ENST00000216099.13 | c.623T>C | p.Met208Thr | missense_variant | Exon 5 of 7 | 2 | NM_152426.4 | ENSP00000216099.7 | ||
ENSG00000284554 | ENST00000381568.9 | c.623T>C | p.Met208Thr | missense_variant | Exon 5 of 7 | 1 | ENSP00000370980.4 | |||
APOBEC3D | ENST00000427494.6 | c.211-2314T>C | intron_variant | Intron 2 of 3 | 1 | ENSP00000388017.2 | ||||
APOBEC3D | ENST00000622217.3 | c.35T>C | p.Met12Thr | missense_variant | Exon 2 of 4 | 5 | ENSP00000480718.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251426Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135906
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727234
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.623T>C (p.M208T) alteration is located in exon 5 (coding exon 5) of the APOBEC3D gene. This alteration results from a T to C substitution at nucleotide position 623, causing the methionine (M) at amino acid position 208 to be replaced by a threonine (T). 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