chr8-85463769-AGGAGCCCCGGAGCCCC-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000654303.1(CA3-AS1):n.17_32delGGGGCTCCGGGGCTCC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000559 in 232,482 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000055 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000058 ( 0 hom. )
Consequence
CA3-AS1
ENST00000654303.1 non_coding_transcript_exon
ENST00000654303.1 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.28
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CA3-AS1 | ENST00000654303.1 | n.17_32delGGGGCTCCGGGGCTCC | non_coding_transcript_exon_variant | Exon 1 of 3 | ||||||
CA3-AS1 | ENST00000517697.6 | n.193+443_193+458delGGGGCTCCGGGGCTCC | intron_variant | Intron 1 of 2 | 4 | |||||
CA3-AS1 | ENST00000521761.6 | n.334+797_334+812delGGGGCTCCGGGGCTCC | intron_variant | Intron 1 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000546 AC: 8AN: 146586Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000583 AC: 5AN: 85810Hom.: 0 AF XY: 0.0000213 AC XY: 1AN XY: 47016
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GnomAD4 genome AF: 0.0000545 AC: 8AN: 146672Hom.: 0 Cov.: 0 AF XY: 0.0000559 AC XY: 4AN XY: 71516
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at