chr1-219915470-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_018713.3(SLC30A10):c.1437T>C(p.Tyr479=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
SLC30A10
NM_018713.3 synonymous
NM_018713.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.768
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 1-219915470-A-G is Benign according to our data. Variant chr1-219915470-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1626137.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A10 | NM_018713.3 | c.1437T>C | p.Tyr479= | synonymous_variant | 4/4 | ENST00000366926.4 | |
SLC30A10 | NM_001376929.1 | c.1248T>C | p.Tyr416= | synonymous_variant | 4/4 | ||
SLC30A10 | NM_001416004.1 | c.762T>C | p.Tyr254= | synonymous_variant | 3/3 | ||
SLC30A10 | NM_001416005.1 | c.762T>C | p.Tyr254= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A10 | ENST00000366926.4 | c.1437T>C | p.Tyr479= | synonymous_variant | 4/4 | 1 | NM_018713.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152264Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251040Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135652
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GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727196
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74394
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at