chr19-46838732-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004069.6(AP2S1):c.327+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000918 in 1,612,762 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★★).
Frequency
Consequence
NM_004069.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP2S1 | NM_004069.6 | c.327+8C>T | splice_region_variant, intron_variant | ENST00000263270.11 | NP_004060.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AP2S1 | ENST00000263270.11 | c.327+8C>T | splice_region_variant, intron_variant | 1 | NM_004069.6 | ENSP00000263270 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152150Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250760Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135560
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1460612Hom.: 0 Cov.: 30 AF XY: 0.0000798 AC XY: 58AN XY: 726658
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152150Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74326
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
AP2S1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 01, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at