11-66235408-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_018026.4(PACS1):c.2207+5G>T variant causes a splice region, intron change. The variant allele was found at a frequency of 0.000000687 in 1,455,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_018026.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PACS1 | NM_018026.4 | c.2207+5G>T | splice_region_variant, intron_variant | Intron 18 of 23 | ENST00000320580.9 | NP_060496.2 | ||
PACS1 | XM_011545162.2 | c.1913+5G>T | splice_region_variant, intron_variant | Intron 18 of 23 | XP_011543464.2 | |||
PACS1 | XM_011545164.3 | c.1868+5G>T | splice_region_variant, intron_variant | Intron 18 of 23 | XP_011543466.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PACS1 | ENST00000320580.9 | c.2207+5G>T | splice_region_variant, intron_variant | Intron 18 of 23 | 1 | NM_018026.4 | ENSP00000316454.4 | |||
PACS1 | ENST00000529757.5 | c.815+5G>T | splice_region_variant, intron_variant | Intron 7 of 12 | 1 | ENSP00000432858.1 | ||||
PACS1 | ENST00000529795.1 | n.339G>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
PACS1 | ENST00000676419.1 | n.244+5G>T | splice_region_variant, intron_variant | Intron 3 of 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455888Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 724544
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.