chr15-82659655-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001278512.2(AP3B2):c.3211C>T(p.Arg1071Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,613,916 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1071Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001278512.2 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 |
---|---|---|---|---|---|---|---|
AP3B2 | NM_001278512.2 | c.3211C>T | p.Arg1071Trp | missense_variant | 27/27 | ENST00000535359.6 | |
CPEB1-AS1 | NR_046096.1 | n.1328+9509G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP3B2 | ENST00000535359.6 | c.3211C>T | p.Arg1071Trp | missense_variant | 27/27 | 1 | NM_001278512.2 | ||
CPEB1-AS1 | ENST00000560650.1 | n.1328+9509G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000624 AC: 95AN: 152160Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000189 AC: 47AN: 249108Hom.: 1 AF XY: 0.000178 AC XY: 24AN XY: 135138
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461638Hom.: 0 Cov.: 31 AF XY: 0.0000894 AC XY: 65AN XY: 727102
GnomAD4 genome AF: 0.000624 AC: 95AN: 152278Hom.: 1 Cov.: 32 AF XY: 0.000698 AC XY: 52AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at