12-102958393-CGCAGCAGCAGCAGCAGCAGCAGCAGCA-CGCA
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_004316.4(ASCL1):c.163_186delCAGCAGCAGCAGCAGCAGCAGCAG(p.Gln55_Gln62del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00049 in 1,507,148 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004316.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASCL1 | NM_004316.4 | c.163_186delCAGCAGCAGCAGCAGCAGCAGCAG | p.Gln55_Gln62del | conservative_inframe_deletion | Exon 1 of 2 | ENST00000266744.4 | NP_004307.2 | |
PAH | NM_001354304.2 | c.-318_-295delTGCTGCTGCTGCTGCTGCTGCTGC | 5_prime_UTR_variant | Exon 1 of 14 | NP_001341233.1 | |||
PAH | n.102958417_102958394delTGCTGCTGCTGCTGCTGCTGCTGC | bidirectional_gene_fusion |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASCL1 | ENST00000266744.4 | c.163_186delCAGCAGCAGCAGCAGCAGCAGCAG | p.Gln55_Gln62del | conservative_inframe_deletion | Exon 1 of 2 | 1 | NM_004316.4 | ENSP00000266744.3 | ||
PAH | ENST00000547319.1 | n.-7_17delTGCTGCTGCTGCTGCTGCTGCTGC | non_coding_transcript_exon_variant | Exon 1 of 3 | 4 | |||||
PAH | ENST00000551337.5 | c.-318_-295delTGCTGCTGCTGCTGCTGCTGCTGC | upstream_gene_variant | 3 | ENSP00000447620.1 | |||||
PAH | ENST00000547319.1 | n.-7_17delTGCTGCTGCTGCTGCTGCTGCTGC | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000313 AC: 47AN: 150120Hom.: 0 Cov.: 0
GnomAD4 exome AF: 0.000510 AC: 692AN: 1356938Hom.: 0 AF XY: 0.000496 AC XY: 332AN XY: 669234
GnomAD4 genome AF: 0.000313 AC: 47AN: 150210Hom.: 0 Cov.: 0 AF XY: 0.000355 AC XY: 26AN XY: 73326
ClinVar
Submissions by phenotype
not specified Benign:1
- -
ASCL1-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at