NM_003664.5:c.2016T>C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_003664.5(AP3B1):c.2016T>C(p.Ala672Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,612,438 control chromosomes in the GnomAD database, including 44,621 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003664.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP3B1 | NM_003664.5 | c.2016T>C | p.Ala672Ala | synonymous_variant | Exon 18 of 27 | ENST00000255194.11 | NP_003655.3 | |
AP3B1 | NM_001271769.2 | c.1869T>C | p.Ala623Ala | synonymous_variant | Exon 18 of 27 | NP_001258698.1 | ||
AP3B1 | NM_001410752.1 | c.2016T>C | p.Ala672Ala | synonymous_variant | Exon 18 of 23 | NP_001397681.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.233 AC: 35496AN: 152032Hom.: 4349 Cov.: 32
GnomAD3 exomes AF: 0.213 AC: 53518AN: 251274Hom.: 6284 AF XY: 0.205 AC XY: 27822AN XY: 135822
GnomAD4 exome AF: 0.229 AC: 334316AN: 1460288Hom.: 40268 Cov.: 32 AF XY: 0.225 AC XY: 163524AN XY: 726512
GnomAD4 genome AF: 0.234 AC: 35534AN: 152150Hom.: 4353 Cov.: 32 AF XY: 0.229 AC XY: 17064AN XY: 74394
ClinVar
Submissions by phenotype
not specified Benign:4
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Ala672Ala in exon 18 of AP3B1: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 25.8% (1135/4406) o f African American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs42360). -
This variant is classified as Benign based on local population frequency. This variant was detected in 46% of patients studied by a panel of primary immunodeficiencies. Number of patients: 44. Only high quality variants are reported. -
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not provided Benign:2Other:1
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Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
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Hermansky-Pudlak syndrome 2 Benign:1
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Hermansky-Pudlak syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at