NM_001039569.2:c.429+51_429+53dupATG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001039569.2(AP1S3):c.429+51_429+53dupATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 1,529,558 control chromosomes in the GnomAD database, including 16,098 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001039569.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP1S3 | NM_001039569.2 | c.429+51_429+53dupATG | intron_variant | Intron 4 of 4 | ENST00000396654.7 | NP_001034658.1 | ||
AP1S3 | XM_011510600.4 | c.292-6412_292-6410dupATG | intron_variant | Intron 3 of 3 | XP_011508902.1 | |||
AP1S3 | NR_110905.2 | n.600+51_600+53dupATG | intron_variant | Intron 5 of 5 | ||||
AP1S3 | NR_110906.2 | n.452+51_452+53dupATG | intron_variant | Intron 3 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AP1S3 | ENST00000396654.7 | c.429+51_429+53dupATG | intron_variant | Intron 4 of 4 | 2 | NM_001039569.2 | ENSP00000379891.2 | |||
ENSG00000286239 | ENST00000650969.1 | n.*1393+51_*1393+53dupATG | intron_variant | Intron 16 of 16 | ENSP00000498456.1 |
Frequencies
GnomAD3 genomes AF: 0.216 AC: 32544AN: 150776Hom.: 6536 Cov.: 0
GnomAD3 exomes AF: 0.129 AC: 25962AN: 201824Hom.: 2734 AF XY: 0.117 AC XY: 12896AN XY: 109964
GnomAD4 exome AF: 0.0801 AC: 110442AN: 1378662Hom.: 9546 Cov.: 32 AF XY: 0.0804 AC XY: 55119AN XY: 685164
GnomAD4 genome AF: 0.216 AC: 32602AN: 150896Hom.: 6552 Cov.: 0 AF XY: 0.220 AC XY: 16202AN XY: 73678
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 40% of patients studied by a panel of primary immunodeficiencies. Number of patients: 38. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at