rs79634593
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001365088.1(SLC12A6):c.*3400C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00729 in 152,312 control chromosomes in the GnomAD database, including 10 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.*3400C>T | 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.*3400C>T | 3_prime_UTR_variant | Exon 26 of 26 | 1 | NM_001365088.1 | ENSP00000346112.3 | |||
SLC12A6 | ENST00000290209 | c.*3400C>T | 3_prime_UTR_variant | Exon 25 of 25 | 1 | ENSP00000290209.5 | ||||
SLC12A6 | ENST00000676379 | c.*2019C>T | 3_prime_UTR_variant | Exon 26 of 26 | ENSP00000502539.1 |
Frequencies
GnomAD3 genomes AF: 0.00729 AC: 1110AN: 152194Hom.: 10 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 392Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 250
GnomAD4 genome AF: 0.00729 AC: 1110AN: 152312Hom.: 10 Cov.: 33 AF XY: 0.00730 AC XY: 544AN XY: 74482
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