rs4532349
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_003664.5(AP3B1):c.1038T>C(p.Asn346Asn) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,604,018 control chromosomes in the GnomAD database, including 38,199 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003664.5 splice_region, 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 |
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AP3B1 | NM_003664.5 | c.1038T>C | p.Asn346Asn | splice_region_variant, synonymous_variant | Exon 9 of 27 | ENST00000255194.11 | NP_003655.3 | |
AP3B1 | NM_001271769.2 | c.891T>C | p.Asn297Asn | splice_region_variant, synonymous_variant | Exon 9 of 27 | NP_001258698.1 | ||
AP3B1 | NM_001410752.1 | c.1038T>C | p.Asn346Asn | splice_region_variant, synonymous_variant | Exon 9 of 23 | NP_001397681.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.184 AC: 27948AN: 152022Hom.: 2843 Cov.: 32
GnomAD3 exomes AF: 0.194 AC: 48604AN: 251172Hom.: 5258 AF XY: 0.188 AC XY: 25543AN XY: 135744
GnomAD4 exome AF: 0.214 AC: 310203AN: 1451880Hom.: 35352 Cov.: 29 AF XY: 0.211 AC XY: 152200AN XY: 722954
GnomAD4 genome AF: 0.184 AC: 27972AN: 152138Hom.: 2847 Cov.: 32 AF XY: 0.182 AC XY: 13499AN XY: 74374
ClinVar
Submissions by phenotype
not specified Benign:4
This variant is classified as Benign based on local population frequency. This variant was detected in 44% of patients studied by a panel of primary immunodeficiencies. Number of patients: 42. Only high quality variants are reported. -
Benign based on MAF (12-22% in ESP populations) -
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not provided Benign:2Other:1
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