12-1791965-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_172364.5(CACNA2D4):c.*1690C>T variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_172364.5 splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA2D4 | ENST00000382722.10 | c.*1690C>T | splice_region_variant | Exon 38 of 38 | 1 | NM_172364.5 | ENSP00000372169.4 | |||
CACNA2D4 | ENST00000382722 | c.*1690C>T | 3_prime_UTR_variant | Exon 38 of 38 | 1 | NM_172364.5 | ENSP00000372169.4 | |||
CACNA2D4 | ENST00000537784.5 | n.*2297C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 15 of 15 | 1 | ENSP00000440231.2 | ||||
CACNA2D4 | ENST00000537784.5 | n.*2297C>T | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000440231.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 6Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 4
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at