11-66070563-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_018026.4(PACS1):c.77C>T(p.Ala26Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000388 in 1,469,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018026.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PACS1 | NM_018026.4 | c.77C>T | p.Ala26Val | missense_variant | 1/24 | ENST00000320580.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PACS1 | ENST00000320580.9 | c.77C>T | p.Ala26Val | missense_variant | 1/24 | 1 | NM_018026.4 | P2 | |
PACS1 | ENST00000527224.1 | n.201C>T | non_coding_transcript_exon_variant | 1/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000858 AC: 13AN: 151552Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000267 AC: 2AN: 74768Hom.: 0 AF XY: 0.0000233 AC XY: 1AN XY: 42912
GnomAD4 exome AF: 0.0000334 AC: 44AN: 1317528Hom.: 0 Cov.: 31 AF XY: 0.0000277 AC XY: 18AN XY: 649432
GnomAD4 genome AF: 0.0000858 AC: 13AN: 151552Hom.: 0 Cov.: 32 AF XY: 0.0000541 AC XY: 4AN XY: 73992
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at