rs2275707
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018713.3(SLC30A10):c.*744G>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 0.85 in 152,250 control chromosomes in the GnomAD database, including 55,385 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.85 ( 55384 hom., cov: 32)
Exomes 𝑓: 1.0 ( 1 hom. )
Consequence
SLC30A10
NM_018713.3 3_prime_UTR
NM_018713.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0350
Genes affected
SLC30A10 (HGNC:25355): (solute carrier family 30 member 10) This gene is highly expressed in the liver and is inducible by manganese. Its protein product appears to be critical in maintaining manganese levels, and has higher specificity for manganese than zinc. Loss of function mutations appear to result in a pleomorphic phenotype, including dystonia and adult-onset parkinsonism. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 1-219914705-C-A is Benign according to our data. Variant chr1-219914705-C-A is described in ClinVar as [Benign]. Clinvar id is 295578.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A10 | NM_018713.3 | c.*744G>T | 3_prime_UTR_variant | 4/4 | ENST00000366926.4 | ||
SLC30A10 | NM_001376929.1 | c.*744G>T | 3_prime_UTR_variant | 4/4 | |||
SLC30A10 | NM_001416004.1 | c.*744G>T | 3_prime_UTR_variant | 3/3 | |||
SLC30A10 | NM_001416005.1 | c.*744G>T | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A10 | ENST00000366926.4 | c.*744G>T | 3_prime_UTR_variant | 4/4 | 1 | NM_018713.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.850 AC: 129280AN: 152130Hom.: 55341 Cov.: 32
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GnomAD4 exome AF: 1.00 AC: 2AN: 2Hom.: 1 Cov.: 0AC XY: 0AN XY: 0
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GnomAD4 genome ? AF: 0.850 AC: 129378AN: 152248Hom.: 55384 Cov.: 32 AF XY: 0.848 AC XY: 63135AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypermanganesemia with dystonia, polycythemia, and cirrhosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | 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. - |
Computational scores
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Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at