chr2-223765159-C-CCATCAT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001039569.2(AP1S3):c.429+48_429+53dupATGATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 1,558,338 control chromosomes in the GnomAD database, including 146,314 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+48_429+53dupATGATG | intron_variant | Intron 4 of 4 | ENST00000396654.7 | NP_001034658.1 | ||
AP1S3 | XM_011510600.4 | c.292-6415_292-6410dupATGATG | intron_variant | Intron 3 of 3 | XP_011508902.1 | |||
AP1S3 | NR_110905.2 | n.600+48_600+53dupATGATG | intron_variant | Intron 5 of 5 | ||||
AP1S3 | NR_110906.2 | n.452+48_452+53dupATGATG | intron_variant | Intron 3 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AP1S3 | ENST00000396654.7 | c.429+48_429+53dupATGATG | intron_variant | Intron 4 of 4 | 2 | NM_001039569.2 | ENSP00000379891.2 | |||
ENSG00000286239 | ENST00000650969.1 | n.*1393+48_*1393+53dupATGATG | intron_variant | Intron 16 of 16 | ENSP00000498456.1 |
Frequencies
GnomAD3 genomes AF: 0.390 AC: 58744AN: 150760Hom.: 12520 Cov.: 0
GnomAD3 exomes AF: 0.429 AC: 86591AN: 201824Hom.: 18024 AF XY: 0.441 AC XY: 48526AN XY: 109964
GnomAD4 exome AF: 0.449 AC: 631952AN: 1407458Hom.: 133803 Cov.: 32 AF XY: 0.453 AC XY: 317238AN XY: 699748
GnomAD4 genome AF: 0.389 AC: 58744AN: 150880Hom.: 12511 Cov.: 0 AF XY: 0.389 AC XY: 28674AN XY: 73662
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 52% of patients studied by a panel of primary immunodeficiencies. Number of patients: 50. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at