15-34230209-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001365088.1(SLC12A6):c.*3672A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00667 in 173,460 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001365088.1 3_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC12A6 | NM_001365088.1 | c.*3672A>G | 3_prime_UTR_variant | Exon 26 of 26 | ENST00000354181.8 | NP_001352017.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC12A6 | ENST00000354181 | c.*3672A>G | 3_prime_UTR_variant | Exon 26 of 26 | 1 | NM_001365088.1 | ENSP00000346112.3 | |||
SLC12A6 | ENST00000290209 | c.*3672A>G | 3_prime_UTR_variant | Exon 25 of 25 | 1 | ENSP00000290209.5 | ||||
SLC12A6 | ENST00000676379 | c.*2291A>G | 3_prime_UTR_variant | Exon 26 of 26 | ENSP00000502539.1 |
Frequencies
GnomAD3 genomes AF: 0.00651 AC: 990AN: 152156Hom.: 5 Cov.: 33
GnomAD4 exome AF: 0.00798 AC: 169AN: 21186Hom.: 0 Cov.: 0 AF XY: 0.00775 AC XY: 86AN XY: 11090
GnomAD4 genome AF: 0.00649 AC: 988AN: 152274Hom.: 5 Cov.: 33 AF XY: 0.00612 AC XY: 456AN XY: 74452
ClinVar
Submissions by phenotype
Agenesis of the corpus callosum with peripheral neuropathy 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at