2-24820010-CAAG-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_004036.5(ADCY3):c.3354_3356del(p.Phe1118del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,542 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
ADCY3
NM_004036.5 inframe_deletion
NM_004036.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.25
Genes affected
ADCY3 (HGNC:234): (adenylate cyclase 3) This gene encodes adenylyl cyclase 3 which is a membrane-associated enzyme and catalyzes the formation of the secondary messenger cyclic adenosine monophosphate (cAMP). This protein appears to be widely expressed in various human tissues and may be involved in a number of physiological and pathophysiological metabolic processes. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
CENPO (HGNC:28152): (centromere protein O) This gene encodes a component of the interphase centromere complex. The encoded protein is localized to the centromere throughout the cell cycle and is required for bipolar spindle assembly, chromosome segregation and checkpoint signaling during mitosis. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_004036.5. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY3 | NM_004036.5 | c.3354_3356del | p.Phe1118del | inframe_deletion | 22/22 | ENST00000679454.1 | |
CENPO | NM_001322101.2 | c.*699_*701del | 3_prime_UTR_variant | 8/8 | ENST00000380834.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY3 | ENST00000679454.1 | c.3354_3356del | p.Phe1118del | inframe_deletion | 22/22 | NM_004036.5 | P4 | ||
CENPO | ENST00000380834.7 | c.*699_*701del | 3_prime_UTR_variant | 8/8 | 5 | NM_001322101.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248844Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134626
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460424Hom.: 0 AF XY: 0.0000138 AC XY: 10AN XY: 726494
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74300
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ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
BODY MASS INDEX QUANTITATIVE TRAIT LOCUS 19 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Mar 28, 2018 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at