19-16228898-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_032493.4(AP1M1):c.1017C>T(p.Ser339Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000726 in 1,614,132 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 (★).
Frequency
Genomes: 𝑓 0.00055 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00074 ( 1 hom. )
Consequence
AP1M1
NM_032493.4 synonymous
NM_032493.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.688
Genes affected
AP1M1 (HGNC:13667): (adaptor related protein complex 1 subunit mu 1) The protein encoded by this gene is the medium chain of the trans-Golgi network clathrin-associated protein complex AP-1. The other components of this complex are beta-prime-adaptin, gamma-adaptin, and the small chain AP1S1. This complex is located at the Golgi vesicle and links clathrin to receptors in coated vesicles. These vesicles are involved in endocytosis and Golgi processing. Alternatively spliced transcript variants encoding distinct protein isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
Variant 19-16228898-C-T is Benign according to our data. Variant chr19-16228898-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649509.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.688 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP1M1 | NM_032493.4 | c.1017C>T | p.Ser339Ser | synonymous_variant | Exon 9 of 12 | ENST00000291439.8 | NP_115882.1 | |
AP1M1 | NM_001130524.2 | c.1053C>T | p.Ser351Ser | synonymous_variant | Exon 10 of 13 | NP_001123996.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000545 AC: 83AN: 152160Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000601 AC: 151AN: 251318Hom.: 0 AF XY: 0.000537 AC XY: 73AN XY: 135860
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GnomAD4 exome AF: 0.000745 AC: 1089AN: 1461854Hom.: 1 Cov.: 30 AF XY: 0.000760 AC XY: 553AN XY: 727232
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GnomAD4 genome AF: 0.000545 AC: 83AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000470 AC XY: 35AN XY: 74448
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
AP1M1: BP4, BP7 -
Computational scores
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Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at