chr11-66070587-C-CGCAGCAGCA
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_018026.4(PACS1):c.113_121dup(p.Gln38_Gln40dup) variant causes a 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). Synonymous variant affecting the same amino acid position (i.e. P34P) has been classified as Benign.
Frequency
Consequence
NM_018026.4 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PACS1 | NM_018026.4 | c.113_121dup | p.Gln38_Gln40dup | inframe_insertion | 1/24 | ENST00000320580.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PACS1 | ENST00000320580.9 | c.113_121dup | p.Gln38_Gln40dup | inframe_insertion | 1/24 | 1 | NM_018026.4 | P2 | |
PACS1 | ENST00000527224.1 | n.237_245dup | non_coding_transcript_exon_variant | 1/7 | 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
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Jun 26, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 07, 2021 | 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