11-66070587-CGCAGCAGCA-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_018026.4(PACS1):c.113_121delAGCAGCAGC(p.Gln38_Gln40del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000119 in 1,342,466 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018026.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PACS1 | NM_018026.4 | c.113_121delAGCAGCAGC | p.Gln38_Gln40del | disruptive_inframe_deletion | Exon 1 of 24 | ENST00000320580.9 | NP_060496.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PACS1 | ENST00000320580.9 | c.113_121delAGCAGCAGC | p.Gln38_Gln40del | disruptive_inframe_deletion | Exon 1 of 24 | 1 | NM_018026.4 | ENSP00000316454.4 | ||
PACS1 | ENST00000527224.1 | n.237_245delAGCAGCAGC | non_coding_transcript_exon_variant | Exon 1 of 7 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000119 AC: 16AN: 1342466Hom.: 0 AF XY: 0.0000136 AC XY: 9AN XY: 663130
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Schuurs-Hoeijmakers syndrome Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with PACS1-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.113_121del, results in the deletion of 3 amino acid(s) of the PACS1 protein (p.Gln38_Gln40del), but otherwise preserves the integrity of the reading frame. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.