11-66070587-C-CGCA
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_018026.4(PACS1):c.119_121dupAGC(p.Gln40dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,493,842 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_018026.4 disruptive_inframe_insertion
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 |
---|---|---|---|---|---|---|---|---|
PACS1 | NM_018026.4 | c.119_121dupAGC | p.Gln40dup | disruptive_inframe_insertion | 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.119_121dupAGC | p.Gln40dup | disruptive_inframe_insertion | Exon 1 of 24 | 1 | NM_018026.4 | ENSP00000316454.4 | ||
PACS1 | ENST00000527224.1 | n.243_245dupAGC | non_coding_transcript_exon_variant | Exon 1 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000119 AC: 18AN: 151402Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 11AN: 91850Hom.: 0 AF XY: 0.000153 AC XY: 8AN XY: 52414
GnomAD4 exome AF: 0.000134 AC: 180AN: 1342440Hom.: 0 Cov.: 31 AF XY: 0.000146 AC XY: 97AN XY: 663110
GnomAD4 genome AF: 0.000119 AC: 18AN: 151402Hom.: 0 Cov.: 32 AF XY: 0.0000947 AC XY: 7AN XY: 73908
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at