chr12-1792268-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_172364.5(CACNA2D4):c.*1387G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,188 control chromosomes in the GnomAD database, including 16,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_172364.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA2D4 | ENST00000382722 | c.*1387G>A | 3_prime_UTR_variant | Exon 38 of 38 | 1 | NM_172364.5 | ENSP00000372169.4 | |||
CACNA2D4 | ENST00000537784.5 | n.*1994G>A | non_coding_transcript_exon_variant | Exon 15 of 15 | 1 | ENSP00000440231.2 | ||||
CACNA2D4 | ENST00000537784.5 | n.*1994G>A | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000440231.2 | ||||
CACNA2D4 | ENST00000280663.12 | n.5631G>A | non_coding_transcript_exon_variant | Exon 36 of 36 | 2 |
Frequencies
GnomAD3 genomes AF: 0.437 AC: 66413AN: 152046Hom.: 16606 Cov.: 33
GnomAD4 exome AF: 0.667 AC: 16AN: 24Hom.: 5 Cov.: 0 AF XY: 0.650 AC XY: 13AN XY: 20
GnomAD4 genome AF: 0.436 AC: 66419AN: 152164Hom.: 16608 Cov.: 33 AF XY: 0.437 AC XY: 32469AN XY: 74378
ClinVar
Submissions by phenotype
Retinal cone dystrophy 4 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at