11-66070587-C-CGCAGCAGCA
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_018026.4(PACS1):c.113_121dupAGCAGCAGC(p.Gln38_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 0.00000669 in 1,493,874 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_018026.4 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PACS1 | NM_018026.4 | c.113_121dupAGCAGCAGC | p.Gln38_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.113_121dupAGCAGCAGC | p.Gln38_Gln40dup | disruptive_inframe_insertion | Exon 1 of 24 | 1 | NM_018026.4 | ENSP00000316454.4 | ||
PACS1 | ENST00000527224.1 | n.237_245dupAGCAGCAGC | non_coding_transcript_exon_variant | Exon 1 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151402Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000435 AC: 4AN: 91850Hom.: 0 AF XY: 0.0000382 AC XY: 2AN XY: 52414
GnomAD4 exome AF: 0.00000521 AC: 7AN: 1342472Hom.: 0 Cov.: 31 AF XY: 0.00000302 AC XY: 2AN XY: 663130
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151402Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73908
ClinVar
Submissions by phenotype
Schuurs-Hoeijmakers syndrome Uncertain:1
- -
Inborn genetic diseases Benign:1
This alteration is classified as likely 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. -
not provided Benign:1
Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at