chr1-183648195-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_203454.3(APOBEC4):c.587C>G(p.Ser196Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00244 in 1,614,144 control chromosomes in the GnomAD database, including 94 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_203454.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.587C>G | p.Ser196Cys | missense_variant | 2/2 | ENST00000308641.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOBEC4 | ENST00000308641.6 | c.587C>G | p.Ser196Cys | missense_variant | 2/2 | 1 | NM_203454.3 | P1 | |
RGL1 | ENST00000304685.8 | c.-33+11694G>C | intron_variant | 1 | |||||
APOBEC4 | ENST00000481562.1 | n.246-398C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0130 AC: 1975AN: 152166Hom.: 47 Cov.: 32
GnomAD3 exomes AF: 0.00331 AC: 832AN: 251428Hom.: 14 AF XY: 0.00258 AC XY: 351AN XY: 135884
GnomAD4 exome AF: 0.00134 AC: 1961AN: 1461860Hom.: 46 Cov.: 34 AF XY: 0.00113 AC XY: 822AN XY: 727234
GnomAD4 genome ? AF: 0.0130 AC: 1979AN: 152284Hom.: 48 Cov.: 32 AF XY: 0.0122 AC XY: 905AN XY: 74464
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