2-24824539-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004036.5(ADCY3):c.2578-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 1,613,354 control chromosomes in the GnomAD database, including 228,070 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004036.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY3 | NM_004036.5 | c.2578-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000679454.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY3 | ENST00000679454.1 | c.2578-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_004036.5 | P4 | ||||
ADCY3 | ENST00000260600.9 | c.2578-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P4 | ||||
ADCY3 | ENST00000405392.6 | c.2581-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
ADCY3 | ENST00000606682.5 | c.1519-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.483 AC: 73490AN: 152050Hom.: 18939 Cov.: 33
GnomAD3 exomes AF: 0.551 AC: 138427AN: 251200Hom.: 39709 AF XY: 0.548 AC XY: 74378AN XY: 135758
GnomAD4 exome AF: 0.531 AC: 775992AN: 1461186Hom.: 209118 Cov.: 43 AF XY: 0.532 AC XY: 386487AN XY: 726860
GnomAD4 genome AF: 0.483 AC: 73518AN: 152168Hom.: 18952 Cov.: 33 AF XY: 0.488 AC XY: 36333AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at