chr1-183647883-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_203454.3(APOBEC4):c.899A>G(p.Asp300Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00236 in 1,614,144 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_203454.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOBEC4 | NM_203454.3 | c.899A>G | p.Asp300Gly | missense_variant | 2/2 | ENST00000308641.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOBEC4 | ENST00000308641.6 | c.899A>G | p.Asp300Gly | missense_variant | 2/2 | 1 | NM_203454.3 | P1 | |
RGL1 | ENST00000304685.8 | c.-33+11382T>C | intron_variant | 1 | |||||
APOBEC4 | ENST00000481562.1 | n.246-86A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0126 AC: 1914AN: 152136Hom.: 46 Cov.: 32
GnomAD3 exomes AF: 0.00320 AC: 805AN: 251434Hom.: 14 AF XY: 0.00248 AC XY: 337AN XY: 135886
GnomAD4 exome AF: 0.00129 AC: 1890AN: 1461890Hom.: 44 Cov.: 66 AF XY: 0.00109 AC XY: 794AN XY: 727246
GnomAD4 genome ? AF: 0.0126 AC: 1916AN: 152254Hom.: 46 Cov.: 32 AF XY: 0.0118 AC XY: 879AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at